Plants have two ways of interacting with each other: they can compete with each other if they use the same resources; or they can ‘help’ each other in what is known as facilitation, for example, when a larger plant protects a smaller plant in harsh environments. These interactions can vary over several generations in response to changes in the environment or the surrounding plant community. For instance, in plant communities formed by many different species, like in most natural systems, competition usually decreases over time as the plants ‘learn’ to grow together.

In agriculture, intercropping – defined as growing at least two species of crop at the same time on the same field – takes advantage from a reduction in competition. The idea is that planting two species that grow differently together will lead to less competition than having a single crop because the two species will use slightly different resources, or use them at different times. However, intercropping has traditionally overlooked changes in the interactions between plants as a result of the crop species evolving after being grown together for generations. Indeed, farmers that practice intercropping generally use standard seeds that have been bred to produce high yields when planted on their own, in what is known as monoculture. If plants can adapt and become less competitive when they are grown together over several generations, then using these standard seeds might limit the success of intercropping.

Stefan, Engbersen and Schöb wanted to know whether crop species adapt to the levels of plant diversity surrounding them over generations, and if so, how they do it. To find this out, they investigated how competition and facilitation changed when six crop species (wheat, oat, lentil, coriander, flax and camelina) that grow annually were grown together in different combinations over several generations. Stefan, Engbersen and Schöb started off with seeds normally used for growing these crops on their own, and planted them either on their own, or in different combinations of two or four species. They then repeated the experiment over the course of three years, each year using seeds from the previous year, recording both crop yields and changes in how the plants interacted with each other.

The experiments showed that interactions among these annual crops shifted towards reduced competition and/or increased facilitation when the plants were growing alongside the same crops as their parents did in the previous two generations.

Improving and promoting the development of intercropping is essential for agricultural sustainability, as it could offer alternatives to intensive monocultures (crops grown on their own that require increased resources). Stefan, Engbersen and Schöb’s findings are relevant for programmes aimed at developing seeds for intercropping, as they highlight the importance of including diversity when developing these seeds. However, before these results can be used in the field, longer experiments (of more than three generations) in different environments should be carried out to confirm the findings. Another question that remains open is what the mechanisms underlying adaptations to intercropping are: more in-depth research will be needed to determine whether the changes observed have a genetic basis.

Following decades of studies demonstrating the positive relationship between species diversity and plant primary productivity in natural systems (Spehn et al., 2005; Tilman et al., 2001), intercropping, that is growing more than two species in the same field during the same period, has been increasingly considered as a promising option to increase agricultural sustainability (Gurr et al., 2016; Brooker et al., 2015; Vandermeer, 1992). The productivity benefits of increasing species diversity rely on two main mechanisms, namely selection effects and complementarity effects, the latter encompassing both facilitation and niche differentiation (Loreau and Hector, 2001; Hooper et al., 2005). In perennial natural grasslands, complementarity effects have been shown to increase over time due to evolutionary processes (Zuppinger-Dingley et al., 2014; van Moorsel et al., 2019; van Moorsel et al., 2019). Notably, greater species complementarity can result from evolutionary changes (Anderson et al., 2011) — that is changes in gene frequency — or from heritable epigenetic changes (Verhoeven et al., 2016) affecting species traits in response to surrounding plant diversity, which either increases niche differentiation (i.e. reduces competition) or increases facilitation (Schöb et al., 2018; Meilhac et al., 2020).

The mechanisms of selection for plant facilitation remain very poorly understood (Bronstein, 2009; Brooker, 2008). Whereas some facilitative traits characterizing facilitator species are well known in some systems — for example legume species fostering soil nitrogen enrichment (Wright et al., 2017), microclimate amelioration through shading by large canopy (Aguirre et al., 2021), nectar reward to attract pollinators (Losapio et al., 2021) — traits of facilitated species remain much more obscure (Bronstein, 2009). These ‘facilitated’ traits, which allow organisms to benefit from their neighbours, may be a target of evolutionary selection in natural systems (Bronstein, 2009), and it is therefore reasonable to think that they might depend on neighbour identity (Schöb et al., 2018). The neighbour-dependent evolution of facilitation in grassland plant communities was demonstrated by Schöb et al., 2018, who showed that selection for net facilitative interactions was favoured in plant mixtures.

The evolutionary potential of plant–plant interactions in diverse communities has tremendous implications for the diversification of agricultural systems (Isbell et al., 2017). This is of particular relevance for mixed cropping systems, where the use of commercial seeds domesticated and bred for maximum yield in monoculture is the norm (Thrall, 2012). These commercial varieties have been selected to express a particular phenotype or traits that would lead to the best yield in monoculture. Yet the optimal monoculture phenotype might not necessarily be the most adequate to promote positive diversity effects in mixtures, and may actually compromise the diversity benefits (Thrall, 2012; Chen et al., 2021; Chacón-Labella et al., 2019; Wuest et al., 2021; Annicchiarico, 2019). Despite the paramount importance of this question, the yield potential of mixture-adapted varieties is, to our knowledge, unknown, as are the trait differences of monoculture- compared to mixture-adapted crops.

Furthermore, the evolution and occurrence of plant–plant interactions is notably context-dependent (Bertness and Callaway, 1994). This environmental dependence of the direction and strength of plant-plant interactions has been conceptualised as the stress–gradient hypothesis (SGH), which suggests that competition between plants is stronger and more important in benign environments — where resources are abundant — while facilitation is more likely to occur in harsher environments — where resources are scarce (Soliveres et al., 2015; Maestre and Cortina, 2004; Maestre et al., 2009). In the context of intercropping, this means that competition would be the dominant interaction in highly productive systems, and therefore, the benefits of increasing niche differentiation — thereby reducing competition — would be higher (Li et al., 2020; Stefan et al., 2021a). On the other side of the stress gradient, enhanced facilitation in resource-poor, low-productive systems may also increase diversity effects (Soliveres et al., 2015). Therefore, the effect of environmental severity on plant–plant interactions and biodiversity effects in intercropped systems is unclear.

In this project, we determined whether, how, and under which soil fertility conditions crop species adapt over three generations to the level of plant diversity that they are surrounded by. We investigated how plant–plant interactions, that is competition and facilitation, and plant traits changed within different coexistence histories over time, and whether these changes translated into yield benefits. To that end, we conducted an intercropping experiment in Switzerland with six different crop species belonging to four functionally different phylogenetic groups, namely wheat, oat, lentil, flax, camelina, and coriander. These species are commonly cultivated in Europe as monocrops and some of them — for example oat, lentil, camelina — are also partly cultivated in intercrops (Neumann et al., 2007; Kraska et al., 2004). We used commercially available seeds commonly used for monoculture practices and selected, whenever possible, open-pollinated varieties as seed source to provide the genetic variability needed for evolutionary processes to occur. The mesocosms — square plots of 0.25 m² — included monocultures, 13 different 2-species mixtures, four different 4-species mixtures, and isolated single plants, and was replicated in two different fertilizing conditions. To assess potential transgenerational changes, we repeated the experiment over the course of three years with seeds from plants grown from either monocultures, mixtures, or single individual plants of the previous year (Figure 1, Figure 1—figure supplement 1). In the third year, we assessed plant–plant interactions within each community using the Relative Interaction Index (Armas et al., 2004), a symmetrical and standardized index that compares the performance in terms of grain yield of a plant growing in a community to its performance when growing in isolation (Michalet et al., 2014; Schöb et al., 2014) (see Methods). This index takes a plant’s eye view by quantifying plant–plant interaction intensity experienced by crop species in monocultures and mixtures. We therefore directly quantify species complementarity underlying classical biodiversity effects (Armas et al., 2004; Schöb et al., 2018). Yield was also used to derive the metrics of biodiversity effects following the method of Loreau and Hector, 2001. Finally, we measured standard above-ground plant traits — that is plant height, plant width, Specific Leaf Area (SLA), Leaf Dry Matter Content (LDMC), and mass per seed — and investigated whether there was a change in mean and variability at the species and community levels in response to the coexistence history of the community.

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We hypothesized that crop mixtures composed of offspring of plants that had been grown for two generations in the same community type (as their offspring do now) would show increased niche differentiation (i.e. less competition) and/or increased facilitation compared to communities of offspring of plants that had been grown in a different community type (as their offspring do now). We also expected that these changes in plant–plant interactions would lead to changes in complementarity effects in crop mixtures, that is communities with the same coexistence history would show higher complementarity effects than the communities with a different history. We hypothesised that the increased niche differentiation would be due to enhanced character displacement. Finally, following the stress gradient hypothesis (Bertness and Callaway, 1994), we expected more facilitation and/or less competition in conditions of reduced soil fertility.

Results from the third year showed that plant–plant interactions shifted towards increased complementarity, that is weaker competition and/or stronger facilitation — distinguishing between these two mechanisms was not possible in this study — when the plants were growing in the same community types as their two previous generations (Figure 2, Figure 2—figure supplement 1, Supplementary file 1a). More precisely, the net Relative Interaction Index, which compares the performance of focal plants growing in communities to the performance of single plants growing alone — focal plants and single plants having the same coexistence history treatment — was significantly higher (+54% [F=30.4; p-value < 0.001; n=276]) when the offspring was grown in the same community type as their parents did than when they were growing in a community type different to the one of their parents (Figure 2). Pairwise comparisons further showed that this effect of coexistence history was particularly true in mixtures and only a trend in monocultures, for both fertilizing conditions (Supplementary file 1b). This notably demonstrates that in mixtures, mixture-adapted communities (i.e. with the same coexistence history) exhibited less competition and/or more facilitation than monoculture-adapted communities or single-adapted communities (i.e. with a different coexistence history). Furthermore, when looking at the effect of fertilization, we observed that competition was weaker and/or facilitation was stronger in unfertilized plots (Figure 2, Figure 2—figure supplement 1;+64% F=44.5; p-value < 0.001; n=276), which is in accordance with the stress–gradient hypothesis.

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This shift in plant–plant interactions was accompanied by a similar shift in net biodiversity effect (NE) in fertilized plots (Figure 3a, Figure 3—figure supplement 1a). Net biodiversity effect — or overyielding — represents the deviation from the expected yield in the mixture, based on the yield of the corresponding monocultures with the same coexistence history as the focal mixture (Loreau and Hector, 2001). The interaction between fertilization and coexistence history had a significant effect on NE (Supplementary file 1c, [F=9.60, p-value = 0.0023, n=204]). Posthoc pairwise comparisons further showed that under fertilized conditions, across all species combinations, NE was on average 58% higher with the same coexistence history than with a different coexistence history (Figure 3a, Supplementary file 1d p-value of the pairwise comparison: 0.0587). This indicates that in fertilized plots, overyielding of crop mixtures tended to be higher with mixture-adapted individuals compared to monoculture-adapted and single-adapted individuals. In unfertilized plots we did not observe the same result, which suggests that even though the shifts in plant–plant interactions were consistent across fertilizing conditions, overyielding was not. When looking at the partitioning of net effects into complementarity and selection effects (Loreau and Hector, 2001), we observed a significant interaction effect between fertilizer, coexistence history and planted diversity on selection effects (Figure 3—figure supplement 2b, Supplementary file 1c, [F=4.09, p-value = 0.045, n=204]). More precisely, for 4-species mixtures under fertilized conditions, SEs were higher in plant communities composed of offspring of plants that had been grown in the same community type (as their offspring do now) than plant communities of offspring of plants that had been grown in a different community type (+109%, Figure 3—figure supplement 2b, Supplementary file 1c, [p-value of the pairwise comparison: 0.0286]). Coexistence history did not affect complementarity effects (Figure 3—figure supplement 2a, Supplementary file 1c, [F=1.57, p-value = 0.21, n=204]), nor total yield (Figure 3b, Figure 3—figure supplement 3, Figure 3—figure supplement 4, Supplementary file 1f, [F<1, p-value > 0.5, n=276]).

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To investigate the ecological mechanisms behind the shift in plant–plant interactions with coexistence history, we assessed the response of standard above-ground plant traits and compared the average values and coefficients of variation at the species and community levels of single-, monoculture- and mixture-adapted varieties. Results pointed towards a reduction in trait variation at the community level, notably of height and leaf dry matter content (Figure 4): the coefficient of variation of height was lower in plant communities composed of offspring of plants that had been grown in the same community type (as their offspring do now) compared to plant communities of offspring of plants that had been grown in a different community type (–9%, Figure 4d, Supplementary file 1l, [F=3.93, p-value = 0.049, n=271]), and for leaf dry matter content it was 15% lower with the same history compared to a different history (Figure 4e, Supplementary file 1o, [F=4.18, p-value = 0.042, n=271]). Furthermore, the coefficient of variation of mass per seed was also lower under the same history compared to a different history, but this effect was only significant in monocultures (–33%, Figure 4f, Supplementary file 1p, [F=5.48, p-value = 0.020, n=271]). The community-weighted means of plant traits (CWM, calculated at the community level) further suggest that when growing in the same community type as their parents, plants seemed to converge towards taller individuals with lower leaf dry matter content. Indeed, the community-weighted mean of leaf dry matter content was significantly lower in plant communities composed of offspring of plants that had been grown in the same community type compared to plant communities of offspring of plants that had been grown in a different community type (–3%, Figure 4b, Supplementary file 1o, [F=4.33, P-value = 0.039, n=271]); height community-weighted mean was not significantly different between coexistence histories (Figure 4a, Supplementary file 1l, [F<1, p-value = 0.48, n=271]), but at the species level we did observe a consistent increase in plant height under the same coexistence history compared to a different history (Figure 4—figure supplement 1, Figure 4—figure supplement 2, Supplementary file 1g, [F=4.29, p-value = 0.040, n=1,726]). We observed similar consistent responses of leaf dry matter content at the species level (Figure 4—figure supplement 2, Supplementary file 1j).

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Our research demonstrates that, after only two generations, annual crop plant communities composed of offspring of plants that had been grown in the same community type (as their offspring do now) showed reduced competition and/or increased facilitation compared to plant communities of offspring of plants that had been grown in a different community type (as their offspring do now). In fertilized conditions, common coexistence history also increased overyielding, but this was not the case in unfertilized conditions. Furthermore, common coexistence history had no effect on total yield per plot. We further investigated whether character displacement was responsible for this evolution of plant–plant interactions; contrary to our hypothesis, results did not show evidence for character displacement, but rather for character convergence in plant aboveground traits.

The observed shift in plant–plant interactions towards reduced competition and/or increased facilitation is consistent with a grassland study investigating the effects of community evolution on plant–plant interactions (Schöb et al., 2018). However, the lack of response of total yield and biodiversity effects across fertilizing conditions does not agree with several grassland studies examining the effects of common evolution on community productivity and niche differentiation, where it was found that common rapid evolution in plant communities can lead to increases in ecosystem functioning (van Moorsel et al., 2018; Zuppinger-Dingley et al., 2014; van Moorsel et al., 2019; van Moorsel et al., 2021; Meyer et al., 2016; Allan et al., 2011). Only in fertilized plots did we observe a positive effect of common coexistence history on net biodiversity effects (i.e. overyielding), which means that the yield benefit of mixtures compared to monocultures was higher when the plants had been adapted to growing in mixtures (Figure 3). Yet we did not observe a significant increase in complementarity effects in response to common coexistence history (Figure 3—figure supplement 2a, Supplementary file 1c). Surprisingly, selection effects also increased in 4-species mixtures in response to coexistence history (Figure 3—figure supplement 2b). This is unexpected, as selection effects have to our knowledge not been shown to increase over time (Cardinale et al., 2007). However, it might be that this short common coexistence history has favoured a specific species or a specific trait that was particularly plastic or strongly linked to productivity (Colom and Baucom, 2021; Turcotte and Levine, 2016).

The apparent discrepancy between the response of plant–plant interactions and the response of net biodiversity effects to coexistence history can stem from various reasons. First, net biodiversity effects are driven both by complementarity and selection effects Loreau and Hector, 2001; therefore, a reduction in competition does not necessarily lead to an increase in net biodiversity effects, as this can be compensated by concurrent changes in selection effects. Changes in RII should however correlate with complementarity effects, which they do in our study (Figure 5, p-value = 0.033), indicating that reduced competition and/or increased facilitation correlates with higher complementarity effects. Most importantly though, our RII calculations and net biodiversity effects use different reference levels, that is the single plant vs the monoculture. Indeed, the biodiversity effect calculations ignore the intensity of intra-specific competition and only assess changes in plant–plant interactions from monoculture to mixture, while RII calculations quantify plant–plant interaction intensity in monocultures and mixtures and therefore also allow to assess effects of coexistence history on intra-specific interactions. This can explain why the effect of coexistence history on plant interactions between individuals (quantified through RII) might diverge from the effects of coexistence history on the diversification of a monospecific community (quantified through the net biodiversity effect, complementarity effect or selection effect). Finally, we also think that the limited timeframe of this study — two generations — might be a reason for the lack of more significant changes in total yield and emphasize the need for longer-term research to confirm the trend identified at the individual level.

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Further investigation is also needed to understand the context–dependence of the effects of common coexistence history, notably when reflecting on the important role of fertilization in our results. Our findings are consistent with several recent studies demonstrating that biodiversity effects are higher in high-inputs systems (Chen et al., 2021; Li et al., 2020; Stefan et al., 2021b), and emphasize the role of fertilization in driving yield benefits in diverse crop communities. Indeed, by promoting crop growth and, consequently, higher competition between plants, fertilization may foster higher benefits of niche differentiation — that is reduced competition — in mixtures (Bertness and Callaway, 1994; Stefan et al., 2021a; Goldberg and Novoplansky, 1997).

Overall, increases in biodiversity effects are associated with changes in species traits in response to surrounding plant diversity (Zuppinger-Dingley et al., 2014; Schöb et al., 2018; Abakumova et al., 2016). Traditional hypotheses of trait and niche theory indeed predict that when several species co-occur closely together, selection over generations would favour character displacement that would reduce resource overlap and consequently increase niche differentiation (Pfennig and Pfennig, 2009; Losos, 2000). Surprisingly, here we found the reverse and observed that a common coexistence history led to a reduction in trait variation, which would suggest a decrease in niche differentiation. Furthermore, functional diversity — calculated as the volume occupied in the space of the traits considered in this study (Petchey and Gaston, 2002) — did not respond to common coexistence history (Figure 6—figure supplement 1, Supplementary file 1q). While surprising, this result is not unheard of Colom and Baucom, 2021; Fox and Vasseur, 2000; Grant, 1972; Weedon and Finckh, 2021; notably, because competition for light is asymmetrical, plant height generally converges towards increased plant height in species-rich communities, as a response to a denser and taller canopy (Lipowsky et al., 1972; Falster and Westoby, 2003). Leaf traits in constrast are usually diverging Lipowsky et al., 1972; this was not the case in our study, where we found convergence towards taller plants with lower leaf dry matter content in response to common coexistence history, that is soft leaves associated with rapid biomass production (Diaz et al., 2016), and consequently less resource-conservative strategies (Reich and Cornelissen, 2014). Lower leaf dry matter content has recently been associated with lower parental or ambient competition (Puy et al., 2021b), which is consistent with our results of plant–plant interaction intensities. The traits examined here did not allow to understand the mechanisms behind the observed reduction in competition; we suggest that other traits or processes not measured in this experiment might have responded to the coexistence history treatment. Notably, there could be a shift in belowground traits, such as root-associated traits (Puy et al., 2021b), or temporal differentiation of resource capture (Engbersen et al., 2021), such as light. We indeed observed a significant increase in light capture ability in communities with a common coexistence history compared to the same communities but with a different coexistence history (Figure 6, Supplementary file 1r), which indicates that plants used to growing in the same community during several generations might capture the resources more fully than plants coming from a different community. This suggests increased niche differentiation for light use with a common coexistence history. However, here we only rely on our light interception measurements and suggest more longer term studies to understand changes in the use of other resources, such as nutrients or water, and how this is associated to plant traits. Finally, the limited duration of the study as well as the lack of evolutionary potential of some of the chosen crops might also explain why we did not observe clearer signs of increased niche differentiation with common coexistence history.

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Furthermore, the scope of this study did not allow us to investigate the transgenerational mechanisms behind these changes in plant–plant interactions and traits in response to coexistence history. The adaptation responses might be genetically based and due to natural selection (van Moorsel et al., 2019), as we specifically selected, whenever possible, open-pollinated varieties in order to ensure a maximum amount of genetic variability. This was notably the case for crops that are not standardly used in western European rotations, such as camelina and coriander. Potentially evolutionary mechanisms include sorting out from standing variation, recombination, mutation (Prentis et al., 2008), or heritable epigenetic processes (Rapp and Wendel, 2005; Sentis et al., 2018; Sobral and Sampedro, 2022). Because our study only accounted for two generations, recombination and mutation are unlikely, as these are long-term processes (Hendry et al., 2007). Rapid adaptation from standing genetic variation is a more plausible mechanism, especially in non-standard species with higher initial variation, such as coriander or camelina (Prentis et al., 2008; Herman and Sultan, 2011). Particularly, outcrossing could have occurred in the first year of this experiment, as we had a similar experiment running in the same experimental garden with Spanish varieties from the same species (Chen et al., 2021; Stefan et al., 2021a). However, considering the short timeframe of this study and the low rate of outcrossing in most of our species, we suggest that epigenetic changes — that is stable heritable changes in cytosine methylation — might also have played an important role as potential evolutionary mechanisms (Verhoeven et al., 2016; Sentis et al., 2018; Herman and Sultan, 2011; Cortijo et al., 2014; Van der Graaf et al., 2015; Saze et al., 2003; Springer, 2013; Puy et al., 2021a). Non-genetic mechanisms can also potentially underpin the observed transgenerational adaptive plasticity; these include seed provisioning, which refers to the carbohydrate, lipid, protein, and mineral nutrient reserves allocated by the maternal plant to the developing seed (Steets and Ashman, 2010; Donohue, 2009; Moles and Westoby, 2006), or changes in maternally derived proteins, mRNAs, or in the relative concentrations of hormones (Herman and Sultan, 2011; Sultan, 1996; Dyer et al., 2010). Finally, a recent study demonstrated the transgenerational role of the seed mycobiome — that is fungal seed–endophytes — for improved resilience and adaptive phenotypes in several generations of wheat Vujanovic et al., 2019; thus, heritable transmission of a specific seed mycobiome and/or microbiome might also be a possible non-genetic mechanism (Vivas et al., 2015).

For the first time, our study provides empirical evidence for rapid transgenerational adaptation in response to common coexistence history in annual crop communities. Notably, we demonstrated that when plants were growing in the same diversity setting as their parents did for two generations, plant–plant interactions shifted towards reduced competition and/or increased facilitation. This history effect was particularly true for mixtures and was associated with increased overyielding under fertilized conditions. However, there was no significant increase in total yield and no yield benefits in unfertilized conditions. Common coexistence history did surprisingly not lead to character displacement in mixtures, but we instead observed character convergence towards taller plants with lower leaf dry matter content. While further research is needed to assess the validity of our findings in other environmental conditions and for other species, this research emphasizes the importance of considering transgenerational effects of diversity for crop mixtures. This is particularly relevant for breeding programs and highlights the need of including diversity when breeding for crop mixtures, in order to design varieties that could be specifically adapted for intercropping.

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Author details

1. Laura Stefan

   1. Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
   2. Plant Production Systems, Agroscope, Nyon, Switzerland

   Contribution

   Conceptualization, Data curation, Formal analysis, Investigation, Visualization, Writing - original draft, Writing - review and editing

   For correspondence

   laura.stefan@m4x.org

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-0798-9782

2. Nadine Engbersen

   Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland

   Contribution

   Data curation, Validation, Investigation

   Competing interests

   No competing interests declared

3. Christian Schöb

   1. Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
   2. Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Spain

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Methodology, Project administration

   Competing interests

   No competing interests declared

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