Network structure of resource use and niche overlap within the endophytic microbiome

Matthew Michalska-Smith,Zewei Song,Georgiana May,Seth A Spawn-Lee,Elizabeth T Borer,Zoe A Hansen,Eric W Seabloom,Linda L Kinkel,Mitch Johnson

doi:10.1038/s41396-021-01080-z

Matthew Michalska-Smith, Zewei Song + Show 7 more

Open Access

https://doi.org/10.1038/s41396-021-01080-z

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Abstract

Endophytes often have dramatic effects on their host plants. Characterizing the relationships among members of these communities has focused on identifying the effects of single microbes on their host, but has generally overlooked interactions among the myriad microbes in natural communities as well as potential higher-order interactions. Network analyses offer a powerful means for characterizing patterns of interaction among microbial members of the phytobiome that may be crucial to mediating its assembly and function. We sampled twelve endophytic communities, comparing patterns of niche overlap between coexisting bacteria and fungi to evaluate the effect of nutrient supplementation on local and global competitive network structure. We found that, despite differences in the degree distribution, there were few significant differences in the global network structure of niche-overlap networks following persistent nutrient amendment. Likewise, we found idiosyncratic and weak evidence for higher-order interactions regardless of nutrient treatment. This work provides a first-time characterization of niche-overlap network structure in endophytic communities and serves as a framework for higher-resolution analyses of microbial interaction networks as a consequence and a cause of ecological variation in microbiome function.

Highlights

Persistent nutrient amendment often leads to reduced diversity [1,2,3] and community stability [4], but increased productivity [5]
We found that the addition of NPK to hosts plants altered networks so that the structure of bacterial and fungal interactions became more similar to one another, suggesting that the role of cross-kingdom interactions in community-wide dynamics is altered significantly with plant nutrient conditions
Nutrient amendments reduce inter-kingdom differences When perennial host plants are exposed to long-term NPK amendments, the interaction network patterns among endophytic fungi become more similar to those of co-occurring bacteria

Summary

Introduction

Persistent nutrient amendment (e.g. of nitrogen, phosphorus, potassium, and other essential elements; hereafter “NPK”) often leads to reduced diversity [1,2,3] and community stability [4], but increased productivity [5]. NPK amendment increases both macronutrient (i.e. N, P, and K; 9, 11), and micronutrient (e.g. Ca and Zn; 11) levels within plant leaves, as well as altering plant carbon allocation [15] and production of enzymes [14] and defensive compounds [13] Against this backdrop of widespread direct and indirect effects of NPK amendments on plants and their associated soil communities, recent work has begun to explore the impacts of nutrient amendments on foliar endophytes; [16, 17] Kinkel unpublished). While shifts in resource use among endophytic populations in response to changes in nutrient amendments may not be surprising, the causes of these shifts and their implications for microbiome dynamics and function are unknown [21, 23, 32] It remains to be answered whether or not the extensive effects of nutrient amendment on microbial composition and phenotype extend into the structure of the microbial interaction network

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