Changes in fitness-associated traits due to the stacking of transgenic glyphosate resistance and insect resistance in Brassica napus L

Increasingly, genetically modified crops are being developed to express multiple 'stacked' traits for different types of transgenes, for example, herbicide resistance, insect resistance, crop quality and tolerance to environmental stresses. The release of crops that express multiple traits could result in ecological changes in weedy environments if feral crop plants or hybrids formed with compatible weeds results in more competitive plants outside of agriculture. To examine the effects of combining transgenes, we developed a stacked line of canola (Brassica napus L.) from a segregating F(2) population that expresses both transgenic glyphosate resistance (CP4 EPSPS) and lepidopteran insect resistance (Cry1Ac). Fitness-associated traits were evaluated between this stacked genotype and five other Brassica genotypes in constructed mesocosm plant communities exposed to insect herbivores (Plutella xylostella L.) or glyphosate-drift. Vegetative biomass, seed production and relative fecundity were all reduced in stacked trait plants when compared with non-transgenic plants in control treatments, indicating potential costs of expressing multiple transgenes without selection pressure. Although costs of the transgenes were offset by selective treatment, the stacked genotype continued to produce fewer seeds than either single transgenic line. However, the increase in fitness of the stacked genotype under selective pressure contributed to an increased number of seeds within the mesocosm community carrying unselected, hitchhiking transgenes. These results demonstrate that the stacking of these transgenes in canola results in fitness costs and benefits that are dependent on the type and strength of selection pressure, and could also contribute to changes in plant communities through hitchhiking of unselected traits.     

Ecological risk assessment of transgenic pasture plants: a community gradient modelling approach

The extension of transgene technology to pasture species presents new challenges for ecological risk assessment because, unlike most crops, pasture plants are well adapted for persistence in mixed plant communities and are an important source of invasive species worldwide. Despite this, the impact of transgenic pasture plants on native ecosystems remains relatively unstudied. Here we use a community gradient modelling approach to investigate the performance of subterranean clover containing a nutrition‐enhancing transgene over a range of ecologically important grassland communities at a study site in south‐eastern Australia. Our data, which were collected over a full annual growing season, show that the transgenic clover line has different seedling survival and seed dormancy breakdown rates than the commercial non‐transgenic line, which suggests that transgenic populations will decline faster than non‐transgenic ones in perennial native grassland communities but could, under optimal climatic conditions, have potentially higher growth rates in grazed annual grasslands. These results demonstrate that changes to ecologically important demographic parameters can occur in plants containing transgenes that are not typically considered fitness enhancing, and that genotype by environment interactions and management regimes that impact on these parameters may influence the invasiveness of transgenic plants. Our study also demonstrates the utility of incorporating plant community gradient modelling into ecological risk assessment protocols designed for transgenic pasture plants.     

Bacterial communities associated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart

The effect of transgenic Bt 176 maize on the rhizosphere bacterial community has been studied with a polyphasic approach by comparing the rhizosphere of Bt maize cultivated in greenhouse with that of its non transgenic counterpart grown in the same conditions. In the two plants the bacterial counts of the copiotrophic, oligotrophic and sporeforming bacteria, and the community level catabolic profiling, showed no significant differences; differences between the rhizosphere and bulk soil bacterial communities were evidenced. Automated ribosomal intergenic spacer analysis (ARISA) showed differences also in the rhizosphere communities at different plant ages, as well as between the two plant types. ARISA fingerprinting patterns of soil bacterial communities exposed to root growth solutions, collected from transgenic and non transgenic plants grown in hydroponic conditions, were grouped separately by principal component analysis suggesting that root exudates could determine the selection of different bacterial communities.     

Coexistence and community structure in a consumer resource model with implicit stoichiometry

We combine stoichiometry theory and optimal foraging theory into the MacArthur consumer-resource model. This generates predictions for diet choice, coexistence, and community structure of heterotroph communities. Tradeoffs in consumer resource-garnering traits influence community outcomes. With scarce resources, consumers forage opportunistically for complementary resources and may coexist via tradeoffs in resource encounter rates. In contrast to single currency models, stoichiometry permits multiple equilibria. These alternative stable states occur when tradeoffs in resource encounter rates are stronger than tradeoffs in elemental conversion efficiencies. With abundant resources consumers exhibit partially selective diets for essential resources and may coexist via tradeoffs in elemental conversion efficiencies. These results differ from single currency models, where adaptive diet selection is either opportunistic or selective. Interestingly, communities composed of efficient consumers share many of the same properties as communities based on substitutable resources. However, communities composed of relatively inefficient consumers behave similarly to plant communities as characterized by Tilman’s consumer resource theory. The results of our model indicate that the effects of stoichiometry theory on community ecology are dependent upon both consumer foraging behavior and the nature of resource garnering tradeoffs.     

Abiotic and biotic resistance to grass invasion in serpentine annual plant communities

Biological invasions severely impact native plant communities, causing dramatic shifts in species composition and the restriction of native species to spatially isolated refuges. Competition from resident species and the interaction between resource limitation and competition have been overlooked as mechanisms of community resistance in refugia habitats. We examined the importance of these factors in determining the resistance of California serpentine plant communities to invasion by three common European grasses, Avena barbata, Bromus diandrus, and Hordeum murinum. We added seeds of each of these grasses to plots subjected to six levels of resource addition (N, P, Ca, H₂O, all resources together, and a no-addition control) and two levels of competition (with resident community present or removed). Resource limitation and competition had strong effects on the biomass and reproduction of the three invaders. The addition of all resources together combined with the removal of the resident community yielded individual plants that were fourfold to 20-fold larger and sixfold to 20-fold more fecund than plants from control plots. Competitor removal alone yielded invaders that were twofold to sevenfold larger and twofold to ninefold more fecund. N addition alone or in combination with other resources led to a twofold to ninefold increase in the biomass and fecundity of the invaders. No other resource alone significantly affected native or invader performance, suggesting that N was the key limiting resource during our experiment. We found a significant interaction between abiotic and biotic resistance for Bromus, which experienced increased competitive suppression in fertilized plots. The threefold increase in resident biomass with N addition was likely responsible for this result. Our results confirm that serpentine plant communities are severely N limited, which, in combination with competition from resident species, promotes the resistance of these systems to invasions. Our work suggests that better understanding the relative sensitivities of invaders and residents to the physical environment is critical to predicting how abiotic and biotic factors interact to determine community resistance.     

Effects of sugar beet chitinase IV on root-associated fungal community of transgenic silver birch in a field trial

Heterogenous chitinases have been introduced in many plant species with the aim to increase the resistance of plants to fungal diseases. We studied the effects of the heterologous expression of sugar beet chitinase IV on the intensity of ectomycorrhizal (ECM) colonization and the structure of fungal communities in the field trial of 15 transgenic and 8 wild-type silver birch (Betula pendula Roth) genotypes. Fungal sequences were separated in denaturing gradient gel electrophoresis and identified by sequencing the ITS1 region to reveal the operational taxonomic units. ECM colonization was less intense in 7 out of 15 transgenic lines than in the corresponding non-transgenic control plants, but the slight decrease in overall ECM colonization in transgenic lines could not be related to sugar beet chitinase IV expression or total endochitinase activity. One transgenic line showing fairly weak sugar beet chitinase IV expression without significantly increased total endochitinase activity differed significantly from the non-transgenic controls in the structure of fungal community. Five sequences belonging to three different fungal genera (Hebeloma, Inocybe, Laccaria) were indicative of wild-type genotypes, and one sequence (Lactarius) indicated one transgenic line. In cluster analysis, the non-transgenic control grouped together with the transgenic lines indicating that genotype was a more important factor determining the structure of fungal communities than the transgenic status of the plants. With the tested birch lines, no clear evidence for the effect of the heterologous expression of sugar beet chitinase IV on ECM colonization or the structure of fungal community was found.     

Elevated carbon dioxide is predicted to promote coexistence among competing species in a trait‐based model

Differential species responses to atmospheric CO₂ concentration (C_a) could lead to quantitative changes in competition among species and community composition, with flow‐on effects for ecosystem function. However, there has been little theoretical analysis of how elevated C_a (eC_a) will affect plant competition, or how composition of plant communities might change. Such theoretical analysis is needed for developing testable hypotheses to frame experimental research. Here, we investigated theoretically how plant competition might change under eC_a by implementing two alternative competition theories, resource use theory and resource capture theory, in a plant carbon and nitrogen cycling model. The model makes several novel predictions for the impact of eC_a on plant community composition. Using resource use theory, the model predicts that eC_a is unlikely to change species dominance in competition, but is likely to increase coexistence among species. Using resource capture theory, the model predicts that eC_a may increase community evenness. Collectively, both theories suggest that eC_a will favor coexistence and hence that species diversity should increase with eC_a. Our theoretical analysis leads to a novel hypothesis for the impact of eC_a on plant community composition. This hypothesis has potential to help guide the design and interpretation of eC_a experiments.     

Resource availability mediates the importance of priority effects in plant community assembly and ecosystem function

Assembly history, including the order in which species arrive into a community, can influence long‐term community structure; however we know less about how timing of species arrival may alter assembly especially under varying resource conditions. To explore how the timing of species arrival interacts with resource availability to alter community assembly, we constructed experimental plant communities and manipulated the interval between plantings of groups of seedlings (0, 5, 10, 15 or 20 days) at low and high levels of soil nutrient supply. To see if community changes influenced ecosystem‐scale processes, we measured parameters across the plant–soil continuum (e.g. plant biomass and net ecosystem carbon dioxide exchange). We found that the timing of species arrival had a large impact on community assembly, but the size of the effect depended on soil fertility. As planting interval increased, plant communities diverged further from the control, but the divergence was stronger at high than at low nutrient supply. Our data suggest that at high nutrient supply, early‐planted species preempted light resources more quickly, thus preventing the successful establishment of later arriving species even at short planting intervals. Finally, we found that assembly related divergence in plant communities scaled to impact ecosystem‐level characteristics such as green leaf chemistry, but had little effect on total community biomass and net ecosystem exchange of CO₂ and water vapor. Our data indicate that the effect of a stochastic factor, here the timing of species arrival on community composition, depends on the resource level under which the community assembles.     

Strategies for antiviral resistance in transgenic plants

Genetic engineering offers a means of incorporating new virus resistance traits into existing desirable plant cultivars. The initial attempts to create transgenes conferring virus resistance were based on the pathogen-derived resistance concept. The expression of the viral coat protein gene in transgenic plants was shown to induce protective effects similar to classical cross protection, and was therefore distinguished as 'coat-protein-mediated' protection. Since then, a large variety of viral sequences encoding structural and non-structural proteins were shown to confer resistance. Subsequently, non-coding viral RNA was shown to be a potential trigger for virus resistance in transgenic plants, which led to the discovery of a novel innate resistance in plants, RNA silencing. Apart from the majority of pathogen-derived resistance strategies, alternative strategies involving virus-specific antibodies have been successfully applied. In a separate section, efforts to combat viroids in transgenic plants are highlighted. In a final summarizing section, the potential risks involved in the introduction of transgenic crops and the specifics of the approaches used will be discussed.     

Refuge-mediated apparent competition in plant–consumer interactions

At the intersection of consumer behaviour and plant competition is the concept of refuge-mediated apparent competition: an indirect interaction whereby plants provide a refuge for a shared consumer, subsequently increasing consumer pressure on another plant species. Here, we use a simple model and empirical examples to develop and illustrate the concept of refuge-mediated apparent competition. We find that the likelihood that an inferior competitor will succeed via refuge-mediated apparent competition is greater when competitors have similar resource requirements and when consumers exhibit a strong response to the refuge and high attack rates on the superior competitor. Refuge-mediated apparent competition may create an emergent Allee effect, such that a species invades only if it is sufficiently abundant to alter consumer impact on resident species. This indirect interaction may help explain unresolved patterns observed in biological invasion, such as the different physical structure of invasive exotic plants, the lag phase, and the failure of restoration efforts. Given the ubiquity of refuge-seeking behaviour by consumers and the ability of consumers to alter the outcome of direct competition among plants, refuge-mediated apparent competition may be an underappreciated mechanism affecting the composition and diversity of plant communities.
Ecology Letters (2010) 13: 11–20     

Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus)

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.     

放牧对内蒙古锡林河流域草地群落植物茎叶生物量资源分配的影响

以内蒙古锡林河流域沿水分梯度分布的灰脉苔草(Carex appendiculata)、贝加尔针茅(Stipa baicalensis)、羊草(Leymus chinensis)、大针茅(Stipa grandis)、小叶锦鸡儿(Caragana microphylla)和冷蒿(Artemisia frigida) 6个草地群落为对象, 研究了围封禁牧与放牧样地中144个共有植物种的高度、丛幅面积、茎、叶和株(丛)生物量、茎叶比等性状。结果表明: 1)在个体水平上, 放牧样地中植物的生殖枝高度、营养枝高度、丛幅面积、单株(丛)生物量、茎、叶生物量和茎叶比均显著低于围封禁牧样地, 植物在放牧干扰下表现出明显的小型化现象; 2)在群落水平上, 放牧亦显著降低了群落总生物量和茎、叶生物量; 3)过度放牧显著改变了物种的资源分配策略, 使生物量向叶的分配比例增加, 向茎的分配比例减少。资源优先向同化器官分配可能是植物对长期放牧干扰的一种重要适应对策; 4)轻度放牧对物种的资源分配没有显著影响, 单株(丛)生物量和群落茎、叶及总生物量均表现出增加趋势, 这与过度放牧的影响正好相反。过度放牧引起的植物个体小型化改变了生态系统中物种的资源分配策略, 进而对生态系统功能产生重要的影响。     

Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.     

A Mechanistic Study of Plant and Microbial Controls over R* for Nitrogen in an Annual Grassland

Differences in species'' abilities to capture resources can drive competitive hierarchies, successional dynamics, community diversity, and invasions. To investigate mechanisms of resource competition within a nitrogen (N) limited California grassland community, we established a manipulative experiment using an R* framework. R* theory holds that better competitors within a N limited community should better depress available N in monoculture plots and obtain higher abundance in mixture plots. We asked whether (1) plant uptake or (2) plant species influences on microbial dynamics were the primary drivers of available soil N levels in this system where N structures plant communities. To disentangle the relative roles of plant uptake and microbially-mediated processes in resource competition, we quantified soil N dynamics as well as N pools in plant and microbial biomass in monoculture plots of 11 native or exotic annual grassland plants over one growing season. We found a negative correlation between plant N content and soil dissolved inorganic nitrogen (DIN, our measure of R*), suggesting that plant uptake drives R*. In contrast, we found no relationship between microbial biomass N or potential net N mineralization and DIN. We conclude that while plant-microbial interactions may have altered the overall quantity of N that plants take up, the relationship between species'' abundance and available N in monoculture was largely driven by plant N uptake in this first year of growth.     

Importance of plant traits and herbivory for invasiveness of Phragmites australis (Poaceae)

Biological invasions change native plant communities, but theory predicting whether introductions create naturalized or invasive species is lacking. Focusing on either plant traits or interactions of introduced plants with native biota creates unreliable results, and improvements may require integration of trait- and interaction-based approaches. To assess the importance of plant traits and herbivory on invasiveness, we incorporated herbivore effects in comparisons of growth and phenology of invasive Phragmites australis and its native congener P. australis subsp. americanus. Our results were influenced by venue (field or common garden), with extended life span and optimized leaf-age structure of introduced P. australis indicating greater potential for resource capture. Attack by introduced gallflies affected expression of plant traits, but we found no consistent effect of aphid attack. Origin did not affect leaf emergence or stem height, but preferential gallfly attack stunted native P. australis and delayed senescence. Greater resource capture and lower attack by nonnative herbivores could give introduced P. australis an advantage over the native subspecies. Our results demonstrating the importance of plant traits as well as their modification by interactions with natural enemies questions whether the outcome of plant introductions can be predicted.     

转基因杨树林下种植转基因棉花对转基因杨棉复合系统内节肢动物群落多样性的影响

【目的】转Bt基因棉花和转Bt基因杨树在我国已推广使用。本研究的目的是调查和分析不同转基因杨棉复合系统内地上节肢动物群落多样性变化,为转基因杨树大规模应用提供生态安全方面的数据。【方法】2019年4-10月,在河北任丘采取欧洲黑杨Populus nigra林下种植转基因棉花Gossypium hirsutum的模式,设置转基因杨树 转基因棉花(复合生态系统1)和非转基因杨树-转基因棉花(复合生态系统2)两种杨棉复合系统,调查杨树和棉花地上部植株节肢动物种类和个体数量,比较节肢动物各功能群的物种数量和个体数量以及香农指数、优势集中性指数、均匀度指数等群落多样性指数,并测定了转基因杨树和棉花叶片Bt蛋白含量。【结果】复合生态系统1中转基因杨树和棉花各自植株上鳞翅目种群累计个体数均显著低于复合生态系统2相应植株上的个体数量。转基因杨树上叶甲类累计个体数量显著高于非转基因杨树上的,寄生蜂类累计个体数量则显著低于非转基因杨树上的。在6月5日、6月21日和9月7日的调查中,转基因杨树上的节肢动物群落香农指数显著高于非转基因杨树上的。除鳞翅目害虫外,2个复合系统中棉株上节肢动物各功能群累计个体数量无显著性差异,香农指数、优势集中性指数和均匀度指数随时间变化的趋势基本一致且同一调查时间无显著性差异,仅在8月17调查中复合生态系统1中棉株上节肢动物香农指数显著高于复合生态系统2棉株上的。将杨树和棉花上节肢动物各类群累计数量相加作为系统整体,复合生态系统1和复合生态系统2在香农指数、优势集中性指数和均匀度指数数值上无显著差异。在调查后期,2个复合系统中节肢动物种群均向杨树叶片聚集。转基因棉花叶片Bt蛋白含量在各调查期均显著高于转基因杨树叶片的。【结论】转基因杨树对靶标害虫种群数量有较好的控制作用,对同系统内棉花上鳞翅目害虫数量亦有协同控制作用。转基因杨棉复合系统中地上节肢动物群落结构稳定,对系统内棉花地上部节肢动物群落多样性无显著影响。靶标害虫对转Bt基因杨树的抗性发展需持续监测。     

Positive interactions, discontinuous transitions and species coexistence in plant communities

The population and community level consequences of positive interactions between plants remain poorly explored. In this study we incorporate positive resource-mediated interactions in classic resource competition theory and investigate the main consequences for plant population dynamics and species coexistence. We focus on plant communities for which water infiltration rates exhibit positive dependency on plant biomass and where plant responses can be improved by shading, particularly under water limiting conditions. We show that the effects of these two resource-mediated positive interactions are similar and additive. We predict that positive interactions shift the transition points between different species compositions along environmental gradients and that realized niche widths will expand or shrink. Furthermore, continuous transitions between different community compositions can become discontinuous and bistability or tristability can occur. Moreover, increased infiltration rates may give rise to a new potential coexistence mechanism that we call controlled facilitation.     

植物邻体间的正相互作用

植物间的正负相互作用是构建植被群落的重要因素,也是群落生态学研究的中心内容之一。近20a来,植物间正相互作用的研究得到快速发展。综述了正相互作用的定义,不同植物群落中的直接、间接正相互作用及其发生机制,正相互作用研究的实验和模型方法,正负相互作用随胁迫梯度的变化及正相互作用对群落构建的影响。探讨了正相互作用研究前景:(1)进一步理解正负相互作用的平衡及其对群落构建的影响;(2)加深对全球变暖背景下的正相互作用的认识;(3)需把正相互作用研究同进化联系起来;(4)充分发挥正相互作用在生态系统中的推动力作用,把正相互作用应用到生态恢复中,为恢复退化生态系统服务。     

Punching above their weight: low-biomass non-native plant species alter soil properties during primary succession

Non‐native invasive plants can greatly alter community and ecosystem properties, but efforts to predict which invasive species have the greatest impacts on these properties have been generally unsuccessful. An hypothesis that has considerable promise for predicting the effects of invasive non‐native plant species is the mass ratio hypothesis (i.e. that dominant species exert the strongest effects). We tested this hypothesis using data from a four year removal experiment in which the presence of two dominant shrub species (one native and the other not), and subordinate plant species, were manipulated in factorial combinations over four years in a primary successional floodplain system. We measured the effects of these manipulations on the plant community, soil nutrient status and soil biota in different trophic levels of the soil food web. Our experiment showed that after four years, low‐biomass non‐native plant species exerted disproportionate belowground effects relative to their contribution to total biomass in the plant community, most notably by increasing soil C, soil microbial biomass, altering soil microbial community structure and increasing the abundance of microbial‐feeding and predatory nematodes. Low‐biomass, non‐native plant species had distinct life history strategies and foliar traits (higher foliar N concentrations and higher leaf area per unit mass) compared with the two dominant shrub species (97% of total plant mass). Our results have several implications for understanding species’ effects in communities and on soil properties. First, high‐biomass species do not necessarily exert the largest impacts on community or soil properties. Second, low‐biomass, inconspicuous non‐native species can influence community composition and have important trophic consequences belowground through effects on soil nutrient status or resource availability to soil biota. Our finding that low‐biomass non‐native species influence belowground community structure and soil properties more profoundly than dominant species demonstrates that the mass ratio hypothesis does not accurately predict the relative effects of different coexisting species on community‐ and ecosystem‐level properties.     

Fertilization alters protistan consumers and parasites in crop-associated microbiomes

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant–soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.