Most microorganisms do not live in isolation; they thrive in communities with large numbers and develop close interactions that generate increased benefits for the group. They can establish a range of relationships, including mutualism, commensalism, synergism, competition, parasitism and predation.
There are two major challenges in sorting out the complex relationships between microorganisms in the ecological systems. First, more than 95% of the microorganisms cannot be artificially cultured, thereby unable to be individually screened by means of experimentation. Second, there exist hundreds of millions of interrelationships between tens of thousands of microorganisms, rendering it impossible to dig into such massive amounts of data through traditional experiments.
However, the Earth Microbiome Project (EMP) dataset—the world’s largest standardized database of microbes on the earth to characterize environments and ecosystems, set up by sampling, sequencing and analysis, has made available ample data resources for scientists.
Recently, the research team led by Prof. XU Jianming from the College of Environmental and Resource Sciences, developed 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 EMP dataset. Their research finding is published in the Microbiome.
This study highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.“With this network, we can gain a better picture of the relationships between microbes, which paves the way for the more insightful understanding of their working mechanism,”said XU Jianming.
Interconnection relationships among 12 environments based on similarity of co-occurrence relationships inferred from a Jaccard distance matrix.
“This research reveals that we should understand things in a systematical manner and deepens our understanding of the significance and diversity of microbes on the earth,” XU Jianming introduced, “The overall resemblance in the network reflects the intensity of potential interaction. Soil and freshwater have more to do with each other than do soil and saltwater. Much of this lies in the water cycle and the effect of water.”
Researchers also stress that the current EMP datasets focus on bacterial and archaeal communities. However, other life forms on the earth (for example plants, animals, and fungi) are also essential in the microbial interactome due to their influences on microbial environments. Therefore, future studies filling a gap for microbial eukaryotes within the EMP framework will help unravel global microbial co-occurrence patterns comprehensively.
Earth microbial co-occurrence network. a Layout and taxonomic profiles of eight domain modules in the Earth microbial co-occurrence network. Modules (M1–M8) are displayed in different colors. b The distribution of vertices from 14 environments in the network where orange indicates the vertices from corresponding environments.