Microbiomes: unifying animal and plant systems through the lens of community ecology theory

Abstract

The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant–fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant–fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant–fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.

Microorganisms as scaffolds of host individuality: an eco-immunity account of the holobiont

“…An emerging area of study is the population dynamics of microorganism transmissions. Animals and plants are islands of microorganisms that interact with each other (Christian et al 2015). Microorganisms are horizontally transferrable through frequent social interactions and also in turn influence social behavior (Archie and Tung 2015).…”

A Multiscale Approach to Plant Disease Using the Metacommunity Concept

“…Further, while our focus is on plant pathogens, pathogenic microbes represent only a small subset of the microbial diversity that comprises the plant microbiome (106,110). The framework we evaluate here holds equal promise for understanding the full community of pathogenic and nonpathogenic plant microbes (35,85,112).…”

Tick microbiome and pathogen acquisition altered by host blood meal

“…Animal hosted microbiome communities are now recognized as essential assemblages that can affect host health, phenotype and disease susceptibility (Gosalbes et al, 2012;Jumpstart Consortium Human Microbiome Project Data Generation Working Group, 2012;Christian et al, 2015). Further, the microbiomes of arthropod vectors of human pathogens can affect the transmission of zoonotic pathogens (Weiss and Aksoy, 2011;Hughes et al, 2014;Narasimhan et al, 2014).…”