Field survey data

Estimate density (individuals per square meter) of Trifolium species in 2x2-m field plots at Bodega Marine Reserve, CA, 2015-201

Data from: Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners

1. Coexistence and diversity in plant communities depend upon outcomes of plant competition. Competition and coexistence can be mediated by abiotic soil nutrient differences as well as by soil microbial communities. The latter effects occur through various mechanisms including negative plant-soil feedbacks, when plants foster the build-up of specialized pathogenic microbes, which ultimately reduce conspecific, but not heterospecific, densities. Microbial mutualists can have generalized associations with host plants, and by associating with multiple species might affect coexistence by conferring different levels of benefit to hosts. 2. We examined the effects of abiotic differences and soil microbial communities, including mutualistic nitrogen-fixing rhizobial bacteria, on coexistence processes and asked whether these interactions inform patterns of co-occurrence in natural communities. We measured plant-soil feedbacks in the greenhouse for three native Trifolium species that either highly co-occurred or were spatially repulsed at our field site. Using size-fractioned soil microbial inocula prepared from field-collected soils, we explored the effect of soil microbes on nodulation and the outcome of competition (RII). We also examined the effects of soil origin (home versus away soil) on the outcome of competition between species. 3. Soil microbes had strong positive effects on plant growth and nodulation. Microbes in general reduced the strength of plant competition relative to competition in sterilized soil and altered the relative strength of interactions with conspecific vs. congeneric neighbours, which often occurred in ways predicted to enhance coexistence. In one pair of highly co-occurring Trifolium, competition was strong in sterilized soils, but these species facilitated one other in presence of the full microbial community. Outcomes of competition in live soil treatments, though quite different from those in sterilized soil, best agreed with the observed field co-occurrence patterns of our three Trifolium species. The net effect of these microbes in general reduced competition while also increasing performance over that in sterilized soil, suggesting a role for soil microbial mutualists in coexistence. 4. Synthesis. Our results demonstrate that interactions between plants and diverse soil communities can alter plant-plant interactions and plant soil feedback. Both can generate frequency-dependence that enables coexistence of congeneric species in natural communities

Greenhouse experiment neighborhood data

Individual biomass, trait, and neighborhood composition for Trifolium greenhouse experimen

Data from: Mutualists stabilize coexistence of congeneric legumes

Coexistence requires that stabilizing niche differences, which cause species to limit themselves more than others, outweigh relative fitness differences that cause competitive exclusion. Interactions with shared mutualists, which can differentially affect host fitness and change in magnitude with host frequency, can satisfy these conditions for coexistence, yet empirical tests of mutualist effects on relative fitness and stabilizing niche differences are largely lacking within the framework of coexistence theory. Here, we show that N-fixing rhizobial mutualists mediate coexistence in four naturally co-occurring, congeneric legume (Trifolium) species. Using experimental greenhouse communities, we quantified relative fitness and stabilizing niche differences for each species in the presence of rhizobia originating from conspecific or congeneric hosts. Rhizobia stabilized coexistence by increasing self-limitation of Trifolium species grown with conspecific rhizobia, thus allowing congeners to increase when rare. Greenhouse-measured invasion growth rates predicted natural, unmanipulated coexistence dynamics of Trifolium species over two years in our field sites. Our results demonstrate that interactions with shared mutualists can stabilize coexistence of closely related species

Trifolium greenhouse competition data

csv file of plant growth data for Trifolium fucatum and Trifolium macraei in greenhouse competition experimen

Trifolium field co-occurrence data

csv file of occurrence values for T. fucatum and T. macraei at Bodega Bay, Californi

Data from: Transcriptomic responses to conspecific and congeneric competition in co-occurring Trifolium

Species coexistence requires differential response to inter- and intraspecific competition, typically conceptualized as niche differentiation. Coexistence of close relatives therefore poses an interesting scenario with regards to niche differentiation since these species generally have many traits in common due to shared ancestry. Native Californian Trifolium assemblages are locally diverse and represent a unique system for understanding competitive interactions among close relatives. We conducted two similar greenhouse studies in which Trifolium fucatum was grown alone, with a conspecific competitor, and with a congeneric competitor (Trifolium macraei). In the first study, we assessed biomass production in T. fucatum, and in the second study we conducted an RNAseq analysis of T. fucatum roots to test for differentially expressed genes that may mediate competitive interactions and potentially coexistence. Compared to plants grown alone, competition (i.e. growth in the same pot) with a conspecific resulted in a greater reduction in biomass than competition with a congener, as predicted by theory. However, competition with a congener resulted in twice as many differentially expressed genes as competition with a conspecific. Annotations of identified genes differentiating congeneric from conspecific competition suggest several functions attributed to interactions with third-party organisms, including nodulation with rhizobial mutualists, and defence responses against pathogens and herbivores. In addition, salt-responsive genes and an iron transporter were differentially expressed in congeneric competition, and comparisons of sodium and iron concentrations in field soils where these species are found showed that T. fucatum occurs in higher sodium and iron microsites than T. macraei. Thus, the transcriptome highlighted abiotic niche axes worth pursuing in future ecological experiments as potential mediators of coexistence. We also found a subset of genes that responded similarly to both congeneric and conspecific competition in both direction and magnitude, indicating some conserved responses to competition, regardless of neighbour identity. Synthesis. Transcriptomic analyses represent novel tools for identifying the molecular mechanisms underlying interactions among species. Working iteratively with ecological experimentation and observation, transcriptomes may allow us to identify novel dimensions of the n-dimensional niche that determine species’ distributions and their ability to coexist