The potential for adaptive plant-microbe feed backs is especially relevant for acquisition of nitrogen , an essential nutrient whose availability in agroecosystems is controlled by interactions between fertility management practices and microbial metabolic processes. Microbial communities supply plant-available N through biological N fixation and mineralization of organic forms, and limit N losses by immobilizing it in soil organic matter. Conventional and organic agroecosystems establish unique contexts in which these transformations occur, shaping microbial communities through system-specific differences in soil N availability and dominant N forms as well as quantity and quality of soil organic matter. Organic fertility inputs such as compost and cover crop residues alter the abundance, diversity, and activity of various nitrogen-cycling microorganisms, while synthetic fertilizers mainly increase the abundance of Acidobacteria and can decrease the abundance of ammonia-oxidizing archaea. Synthetic fertilizers may affect microbial community structure via changes in pH, increasing the abundance of acid-tolerant taxa indirectly through soil acidification, or may alter the relative abundance of specific taxa even when pH is relatively constant. Changes in microbial community structure and activity in bulk soil affect not just the rates but also the outcomes of agriculturally and environmentally relevant Ncycling processes such as denitrification. Roots are also key regulators of N transformations,plastic growing bag leading to higher rates of N cycling that are more closely coupled to plant demand in the rhizosphere than in bulk soil compartments. The maize rhizosphere harbors a distinct denitrifier community and is enriched in functional genes related to nitrogen fixation , ammonification , nitrification , and denitrification relative to soil beyond the influence of roots.Understanding regulation of tight coupling of rhizosphere N cycling processes to plant demand could provide new avenues for more efficient and sustainable N management, particularly in an era of global change.

However, it is necessary to go beyond exploration of individual effects of plant selection and agricultural management on rhizosphere microbial communities and consider how these factors interact. This knowledge can contribute to managing rhizosphere interactions that promote both plant productivity and agroecosystem sustainability. While management-induced shifts in bulk soil microbiomes affect environmental outcomes, plant-regulated rhizosphere communities are more directly relevant to yield outcomes. Improved understanding of how plant selection changes across management systems is thus an essential component of sustainable intensification strategies that decouple agroecosystem productivity from environmental footprints, particularly in organic systems where yields are formed through transformation of natural resources rather than transformation of external synthetic inputs.When management and plant rhizosphere effects shape rhizosphere microbial communities, a number of scenarios are possible: one could be greater than the other , their effects could be additive , or they could interact . Typically, these effects are considered additive , where management shapes bulk soil communities and plant effects act consistently, such that rhizosphere communities are distinct from bulk soil and differ from one another to the same degree as their respective bulk soil communities. However, variation in rhizosphere microbiomes and co-occurrence networks between management systems and the unique responses of bulk soil and rhizosphere bacteria to cropping systems point toward M × R interactions shaping microbial community composition. Nonetheless, the functional significance of these interactive effects on critical functions such as N cycling is complex and remains difficult to predict. For example, biological N fixation is driven in large part by plant demand, but high inputs of synthetic fertilizer reduce rates of biological N fixation, diminishing the role of soil microbial communities in supplying plant nutrients and increasing the potential for reactive N losses. Understanding how the M × R interaction affects ecological functions is thus a knowledge gap of critical agricultural and environmental relevance. Adaptive plant-microbe feed backs in the rhizosphere have been described for natural ecosystems, but whether this can occur in intensively managed agricultural systems where resources are more abundant is less clear. We asked whether adaptation to contrasting management systems shifts the magnitude or direction of the rhizosphere effect on rhizosphere community composition and/or N-cycling functions across systems.

For instance, can the same genotype selectively enrich adaptive functions that increase N mineralization from cover crops and compost when planted in an organic system and also reduce denitrification loss pathways from inorganic fertilizer when planted in a conventional system? We hypothesized that an M × R interaction would result in differences in the magnitude or direction of the rhizosphere effect on microbial community structure and functions and that differences between rhizosphere communities, cooccurrence network structure, or N-cycling processes would reflect adaptive management-system-specific shifts. To test these hypotheses, we investigated microbial community composition and co-occurrence patterns in bulk and rhizosphere samples from a single maize genotype grown in a long-term conventional-organic field trial. We further quantified the abundance of six microbial N-cycling genes as case study for M × R impacts on rhizosphere processes of agricultural relevance. Our approach integrated ordination, differential abundance and indicator species analyses, construction of co-occurrence networks, and quantitative PCR of N-cycling genes to gain a deeper understanding of the factors that shape rhizosphere community and ecological interactions.A greater number of ASVs showed a significant response to plant selection in conventional than organic soil . Five bacterial and five fungal ASVs were differentially abundant between the conventional bulk and rhizosphere soils , as compared to one bacterial and two fungal ASVs in the organic bulk and rhizosphere soils . The number of differentially abundant taxa between the rhizosphere communities of the two systems was at least as great as the number responding to within-system rhizosphere effects . More fungal than bacterial ASVs were differentially abundant between these rhizosphere communities: 24 fungal ASVs but only six bacterial ASVs were significantly different in abundance between CR and OR, indicating strong M × R interactions. The differentially abundant fungi and bacteria were evenly distributed between the two management systems. For fungi, 11 ASVs were more abundant in the rhizosphere of conventional plants and 13 were more abundant in organic.

The Mortierellales were the most-represented order with four ASVs, but these were not disproportionately found in CR or OR .We asked how agricultural management and plant roots act individually and in combination to shape microbial community composition, co-occurrence patterns, and N-cycling functions, and whether this interaction leads to system-specific adaptation. In accordance with known management and rhizosphere effects on microbial community structure and N dynamics in agroecosystems, we observed conventional/organic and bulk/rhizosphere differences in many of the parameters measured. Furthermore, many of our analyses supported the hypothesis that plant selective influence varies with management to shape plantassociated microbial community composition and structure . Management, rhizosphere, and M × R effects on microbial communities are likely mediated in large part by soil physicochemical properties,wholesale grow bags which differed between management systems and soil compartments . Strong effects of management on soil physicochemical properties were visible in the higher NO3-N, P, K, Ca, Na, and SOM levels in the organic system and higher Mg and pH in the conventional system. Rhizosphere soil was depleted in NO3-N, P, and K in both management systems. M, R, and M × R effects on soil properties such as nutrient availability, pH, and organic matter likely contribute greatly to microbial community assembly in these treatments. Significant differences in the direction or magnitude of the rhizosphere effect were observed for bacterial diversity, community composition, and indicator species . Plant roots consistently imposed a strong selective filter, and similarity between rhizosphere communities was greater than similarity between bulk soil communities . Nevertheless, rhizosphere communities still reflected the impacts of management on the contributing microbial pool, and rhizosphere communities were more similar to their corresponding bulk soil communities than to one another . The direction of the rhizosphere effect varied with management for bacterial diversity, indicator species, and community structure. This M × R interaction resulted in rhizosphere bacterial communities that were more similar in diversity, composition, and structure than bulk soil bacterial communities. Rhizosphere bacterial/archaeal diversity was lower in the organic rhizosphere but higher in the conventional rhizosphere compared to bulk soil . Although roots are often thought to impose a selective filter that decreases diversity, higher species richness in the rhizosphere as observed here in the conventional system has been reported elsewhere when plants select for enrichment of certain processes. Here, however, whether functional enrichment is related to selection for increased diversity is unclear. Environmental filtering may account for the fact that bacterial rhizosphere networks were more similar than bulk soil networks. Although it has been hypothesized that niche sharing should lead to greater co-occurrence and thus more densely connected networks in the rhizosphere, this effect was seen only in the bacterial organic networks . Viewed in combination with previous work showing smaller, less densely connected networks in rhizosphere soil, our results suggest that rhizosphere effects on co-occurrence networks, like other metrics of microbial community structure, may well be context- and system-dependent. The magnitude of plant effects on rhizosphere communities also differed between management systems. We generally found greater differences between bulk and rhizosphere community composition in conventional soils compared to organic. Hartman et al. attribute a similar M × R interaction observed in their study of wheat agroecosystems to the application of management practices immediately before root establishment. This explanation may apply here as well, specifically with regard to the spatial scale of cover crop and fertilizer inputs.

Inorganic fertilizer and composted poultry manure were trenched in seed beds and therefore near crop roots, likely favoring divergence of bulk soil and rhizosphere microbial communities. Since cover crops were sown throughout the organic plots, cover cropping-induced changes in microbial community composition were likely similar in the bulk soil and early root zone, whereas emerging roots in the conventional plots would likely have encountered a fertilizer-enriched zone already distinct from most of the bulk soil.We further hypothesized that rhizosphere communities would be enriched in system-specific beneficial taxa and functions of importance for plant adaptation to system-specific soil conditions. Although indicator species analysis revealed system-specific taxa, we cannot definitively conclude whether these taxa are beneficial based on amplicon sequencing data. Three members of the order Myxococcales and two members of the order Burkholderiales were indicators of organic environments, in line with previous studies showing these orders to be organic-system-specific. Two strains of the Anaerolineales, an order that displaces other fermenters under high-nitrate conditions, were indicators of the conventional system. Broad ecological information about soil fungi is limited in comparison to bacteria and archaea, despite extensive specialized literature on pathogens of humans and plants or AMF and other endophytes. Many fungal indicators identified here belong to genera known to be pathogenic on other host species, and these were relatively evenly distributed among environments. The significance of pathogens as indicator species in these systems is unclear, especially for pathogens such as Boeremia exigua, which causes leaf spot on diverse host crops including tomato, the other crop in this rotation, but is not known to cause disease in maize.Mortierella, the most common genus among fungal indicators in this study, are known to be a large genus of saprotrophs. Exophiala equina and Didymella sp. have been reported elsewhere to be associated with plant roots. Fungi are critical drivers of C/N cycling and carbon sequestration in agricultural systems, and linking specific taxa to roles beyond pathogenic interactions will be a valuable expansion of the existing literature. With regard to N-cycling functions, we quantified six genes involved in different steps of the nitrogen cycle, all of which were affected by plant selection and only two of which were differentially selected between systems . The relative abundance of genes relative to one another was similar across treatments, suggesting that no system-specific bottlenecks in the N cycle were observed . The abundances of the nifH, amoA , nirK, nirS, and nosZ genes were higher in the bulk soil, in contrast to previous studies that found the maize rhizosphere was enriched in functional genes related to nitrogen fixation , nitrification , and denitrification. That effect was also observed with the addition of artificial maize root exudates, suggesting that exudates are the main mechanisms influencing microbial N cycling independently of other physicochemical characteristics of the rhizosphere. However, mechanisms other than exudates may be responsible for the discrepancy in the direction of the rhizosphere effect between the present study and the literature: while certain root exudates inhibit nitrification in wheat, sorghum, and rice, this effect has not been shown in maize.