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Planta Med
DOI: 10.1055/a-2420-0270
Original Papers

Medicinal Plant Microbiomes: Factors Affecting Bacterial and Fungal Community Composition

Daniel Zagal
1   Pharmacognosy Institute and Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, Illinois, USA
,
James G. Graham
1   Pharmacognosy Institute and Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, Illinois, USA
,
Jonathan Bisson
1   Pharmacognosy Institute and Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, Illinois, USA
,
Stefan J. Green
2   Genomics and Microbiome Core Facility, Rush University, Chicago, Illinois, USA
,
Guido F. Pauli 
1   Pharmacognosy Institute and Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, Illinois, USA
› Author AffiliationsSupported by: National Center for Complementary and Integrative Health P50 AT0000155
Supported by: National Center for Complementary and Integrative Health T32 AT007533
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Abstract

This exploratory study was designed to identify factors implicating microbial influence on medicinal plant metabolomes. Utilizing a whole-microbiome approach, amplicon sequencing was used to identify the makeup of fungal and bacterial assemblages from endophytic (interior) and epiphytic (external) environments in two different sets of congeneric host-plant pairs, with collection of multiple samples of two medicinal plant species (Actaea racemosa, Rhodiola rosea) and two generic analogs (Actaea rubra, Rhodiola integrifolia). Diversity analysis of microbial assemblages revealed the influence of three primary factors driving variance in microbial community composition: host-plant taxonomy, the compartmentalization of microbial communities within discrete plant parts, and the scale of distance (microhabitat heterogeneity) between sampling locations. These three factors accounted for ~ 60% of variance within and between investigated microbiomes. Across all our collections, bacterial populations were more diverse than fungi (per compartment), and microbial density in epiphytic compartments (aerial parts, rhizosphere) were higher than those of endophytes (leaf and root). These comparative data point to key loci associated with variation between congeneric pairs and plant genera, providing insight into the complex and contrasting relationships found within this multi-kingdom coevolutionary relationship. Although reflective of only a limited set of botanical source materials, these data document the richness of a relatively unexplored component of the plant world and highlight the relevance of a whole-microbiome ecology-driven approach to botanical research and directed natural product investigations.

Keywords

plant microbiome - community composition - endophytes - epiphytes - alpha diversity - beta diversity - Actaea - Rhodiola - Ranunculaceae - Crassulaceae

Supporting Information

    The number of observed features in each plant compartment, as well as a list of differentially abundant microbial taxa across host species and compartments for both bacterial and fungal datasets are available as Supporting Information.

  • Supporting Information


Publication History

Received: 29 June 2024

Accepted after revision: 09 September 2024

Article published online:
24 October 2024

© 2024. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 

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