Microorganisms typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals and humans they associate with. The ability to predict the structure of these complex communities is crucial to understanding and managing them. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states and, ultimately, rationally designing communities de novo.

To examine the geographic patterns in Alnus-associated ectomycorrhizal (ECM) fungal assemblages and determine how they may relate to host plant biogeography, we studied ECM assemblages associated with two Alnus species (Alnus acuminata and Alnus jorullensis) in montane Mexico and compared them with Alnus-associated ECM assemblages located elsewhere in the Americas. ECM root samples were collected from four sites in Mexico (two per host species), identified with ITS and LSU rRNA gene sequences, and assessed using both taxon- (richness, diversity, evenness indices) and sequence divergence-based (UniFrac clustering and significance) analyses. Only 23 ECM taxa were encountered. Clavulina, an ECM lineage never before reported with Alnus, contained the dominant taxon overall. ECM assemblage structure varied between hosts, but UniFrac significance tests indicated that both associated with similar ECM lineage diversity. There was a strikingly high sequence similarity among a diverse array of the ECM taxa in Mexico and those in Alnus forests in Argentina, the United States, and Europe. The Mexican and United States assemblages had greater overlap than those present in Argentina, supporting the host-ECM fungi co-migration hypothesis from a common north temperate origin. Our results indicate that Alnus-associated ECM assemblages have clear patterns in richness and composition across a wide range of geographic locations. Additional data from boreal western North America as well as the eastern United States and Canada will be particularly informative in further understanding the co-biogeographic patterns of Alnus and ECM fungi in the Americas.

SummaryAlnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria and, although their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts.We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus (P) and nitrogen (N) when compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii.At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than that from P. menziesii, whereas potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites. At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host.Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic P acquisition abilities relative to non-Frankia ECM hosts. This shift, in combination with the chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities.

Colonization-competition tradeoffs have been shown to be important determinants of succession in plant and animal communities, but their role in ectomycorrhizal (ECM) fungal communities is not well understood. To experimentally examine whether strong spore-based competitors remain dominant on plant root tips as competition shifts to mycelial-based interactions, we investigated the mycelial competitive interactions among three naturally co-occurring ECM species (Rhizopogon occidentalis, R. salebrosus, and Suillus pungens). Each species was grown alone and in all pair-wise combinations on P. muricata seedlings in experimental microcosms and culture assays. Competitive outcomes were assessed from ECM root tip colonization, soil mycelial abundance, and mycelial growth in culture. In the microcosm experiment, we observed a clear competitive hierarchy of R. salebrosus>R. occidentalis>S. pungens. Competitive effects were also apparent in the culture assays, however, no similar hierarchy was present. These results contrast with our previous findings from spore-based competition, suggesting that ECM competitive outcomes can be life-stage dependent. The differing competitive abilities observed here also showed general correspondence with patterns of ECM succession in Pinus muricata forests, indicating that competitive interactions may significantly influence temporal patterns of ECM community structure.

While the biogeography of Alnus species is well characterized, that of their microbial symbionts remains less well understood. Little is known, for example, about how the genotypic richness of Alnus-associated Frankia bacteria varies at the continental scale, and the richness of Alnus-associated Frankia at tropical latitudes has yet to be explored. In this study, we conducted sequence-based analyses of the nifH gene comparing Frankia found in root nodules of two Alnus species in central Mexico with those associated with two Alnus species in the northwestern United States of America (USA). Similar to Frankia assemblages in northwestern USA and other geographic locations, genotypic richness within the Mexican samples was low, with five genotypes total using a ≥97% nifH sequence similarity cutoff. The vast majority of Mexican sequences belonged to genotypes also very common in northwestern USA Alnus forests, although two novel Mexican genotypes were identified. Phylogenetic analyses confirmed that all of the genotypes present in Mexico belong to larger clades of Alnus-associated Frankia. Genotype-and distance-based community analyses indicated that neither geographic location nor the phylogenetic relationships among hosts are strong predictors of Frankia assemblage structure. Our results suggest that factors other than classic biogeography are more influential in determining the continental-scale distribution and diversity of Alnus-associated Frankia.Résumé : Bien que la biogéographie des espèces d'Alnus soit bien documentée, celle de leurs symbiotes microbiens demeure moins bien comprise. On sait peu de choses par exemple sur la façon avec laquelle la richesse génotypique des bactéries Frankia associées aux Alnus varie à l'échelle continentale; la richesse des Frankia associés aux Alnus aux latitudes tropicales reste à explorer. Dans cette étude, l'auteur a effectué des analyses basées sur le séquençage du gène nifH, en comparant les Frankia trouvés dans les nodules racinaires de deux espèces d'Alnus du centre du Mexique avec ceux associés à deux espèces d'Alnus du nord-ouest américain. Tout comme pour les assemblages des Frankia du nord-ouest américain et autres localités géographiques, la richesse génotypique dans les échantillons du Mexique est faible avec un total de cinq génotypes, en utilisant une coupure de similarité à ≥97 % de la séquence du gène nifH. La grande majorité des séquences mexicaines appartient aux génotypes également communs dans les forêts d'Alnus du Nord-ouest américain, bien qu'on ait identifié deux nouveaux génotypes pour le Mexique. Les analyses phylogénétiques confirment que tous les génotypes présents au Mexique appartiennent à des clades plus larges de Frankia associés aux Alnus. Les analyses de communautés basées sur les génotypes et les distances indiquent que ni la localisation géographique ni les relations phylogénétiques parmi les hôtes ne constituent un moyen robuste de prédiction pour la structure d'assemblage des Frankia. Les résultats suggèrent que des facteurs autres que la b...