**Author details**

**7. Conclusions**

106 Plant Ecology - Traditional Approaches to Recent Trends

In the face of pressure from climate change, contaminated environments, and crop pathogens, agricultural material and food production are currently at risk. Plant-associated microorganisms have important consequences for host health and performance. However, efforts to utilize beneficial microbes in the field have failed to consistently improve crops. The current understanding of interactions between plants and symbiotic microbial communities, the ecological consequences of plant-associated microorganisms and plant-microbial metabolic dynamics are limited. The advent of genomic approaches has helped a great deal in the understanding of the plant-bacterial interactions, but genomic approaches are still insufficient to clearly explain the interactions between plants and pathogens [168]. Approaches using metagenomics and amplicon sequencing coupled with other omics technologies [169] and the development of databases (PHI-based) [170], and metabolomics have enhanced our understanding of plant-bacterial interactions. Plant-microbe ecological communities are affected by plant genotype and environmental factors. The difference between genotypes causes different physiological and immune responses and leads to host-specific microbial communities. Plant root exudates (i.e., sugars, amino acids, organic acids, nucleotides, flavonoids, antimicrobial compounds, and enzymes) shape specific

**Figure 3.** Genomic tools to understand major units of the plant-microbe ecological system. Colored boxes indicate technique tools that can be used to characterize key factors for the corresponding unit. (modified after Kroll et al. [167]).

communities, attract plant growth-promoting colonization, and pathogen infections.

vide new opportunities for enhancing disease management.

In the complex microbial community, we found that specific species could significantly affect the microbial community structure. Via a systems' framework of microbial network analysis, we could identify the "hub species" and "milestone species", which are candidate microbial assemblages for disease management. Network models of plant-associated microbiomes proYing-Ning Ho<sup>1</sup> , Dony Chacko Mathew<sup>2</sup> and Chieh-Chen Huang<sup>2</sup> \*

