Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq

Eman M Khalaf; Anuja Shrestha; Michelle Reid; Benjamin J McFadyen; Manish N Raizada

doi:10.3389/fmicb.2023.1276241

Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq

Front Microbiol. 2023 Dec 21:14:1276241. doi: 10.3389/fmicb.2023.1276241. eCollection 2023.

Authors

Eman M Khalaf^#^{1

2}, Anuja Shrestha^#¹, Michelle Reid¹, Benjamin J McFadyen¹, Manish N Raizada¹

Affiliations

¹ Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
² Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt.

^# Contributed equally.

Abstract

Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.

Keywords: MiSeq; PacBio; conservation; landraces; maize; metagenomics; microbiome; pollen.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was provided by grants from the Grain Farmers of Ontario, Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), and the Natural Sciences and Engineering Research Council of Canada (NSERC).