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

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.

Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route

“…K. intermedia , a member of the pan-American core maize pollen microbiome ( Khalaf et al., 2023 ), was previously shown to antagonize the fungal pathogen Rhizoctonia solani ( Anak et al., 2021 ), and the bacterial pathogen Pseudomonas syringae in kiwifruit ( Tontou et al., 2016 ), but we could not find any reports from the literature of this species having anti- Fg or anti- Fusarium activities. It is also noteworthy that several studies reported that K. intermedia exhibited plant growth-promoting traits ( Vazquez et al., 2000 ; Pallavi and Gupta, 2013 ; Boechat and Carlos, 2020 ; Pratiwi et al., 2020 ).…”

“…Third, greenhouse trials and confocal microscopy provided direct evidence that a subset of these bacteria could defend the style (silks) and/or the resulting seed progeny against anti-GER Fusarium species and their mycotoxins ( Figures 6 – 9 ; Table 3 ). The pollen-associated anti- Fusarium strain used in confocal microscopy (AS541) was assigned to the species Kluyvera intermedia (based on 16S sequencing), which was recently shown by our group, in a parallel PacBio-based microbiome study ( Khalaf et al., 2023 ), to be present in pollen of 15/17 diverse maize accessions. Finally, full-length 16S rRNA-based taxonomic profiling of pollen-associated bacteria showed that the majority of taxa from the major wild ancestor of modern maize were present in at least one post-domestication landrace in the study panel ( Figure 4 ).…”