Background: Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. Results: This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Conclusion: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.

No abstract

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Background: Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes in this context is that they engage in symbiosis with rhizobia, which are abundant in soils and include both symbiotic and non-symbiotic bacterial strains. If and how the capacity of rhizobia to form symbiosis modulates root-associated microbiomes are not well understood. Results: We address this question by inoculating soybean (Glycine max) plants with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens. The noeI mutant produces a defective Nod factor and is thus compromised in its ability to establish functional symbiosis. Compared to soybean plants inoculated with WT rhizobia, plants inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation, and exhibited strong changes in microbiome assembly in the rhizosphere and the rhizoplane. NoeI mutant-inoculated roots exhibited reduced diversity, co-occurrence interactions and a substantial depletion of beneficial microbes on the roots. The effects of the noeI mutation were absent in soils without plants, demonstrating that they are plant dependent. Complementation experiments showed that flavonoid supplementation is sufficient to restore recruitment of beneficial microbes. Conclusion: The results illustrate that the capacity of a rhizobium to form microbial symbiosis dramatically alters root-associated microbiomes, most likely by changing root exudation patterns. The results of this study have important implications for our understanding of the evolution of plant-microbiome interactions in the context of plant-bacterial symbioses.