Crop, genotype, and field environmental conditions shape bacterial and fungal seed epiphytic microbiomes

Abstract

Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and two generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and ITS regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e. generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a “core microbiome” was detected consisting of five bacterial and twelve fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.

Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

“…It has also been shown that lettuce seeds can carry Olpidium virulentus (a Chytridiomycete) resting spores externally on the seed coat where they can eventually colonize the spermosphere and begin to infect the developing root (Maccarone, 2013)-we observed Chytridiomycete reads in cassava spermospheres. Similar to our results, some published core spermospheres have been described to contain Pantoea, Pseudomonas, Massilia, Fusarium, and/or Alternaria (Links et al, 2014;Chen et al, 2016;Klaedtke et al, 2016;Eyre et al, 2019;Chartrel et al, 2021;Moreira et al, 2021).…”

Recent Developments in the Study of Plant Microbiomes

“…However, since it has become clear that the judicious use of these microbiomes may hold the key to reproducibly promoting plant growth in the field, to study and understand seed microbiomes has become more and more important. Although the number of studies of seed microbiomes is relatively limited [ 75 , 115 , 116 , 117 , 118 , 119 , 120 ], there is a very real prospect that seed microbiomes have the ability to be transmitted to, and therefore benefit, the next generation of plants. While bacterial and fungal microbiomes may be present both on the seed surface or endophytically within the seed, it is only the endophytic organisms that can be reliably transmitted to the next generation of plants.…”

Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought

“…Recent work on canola ( Brassica napus L. or B . juncea L.) bacterial communities has begun to correct this knowledge deficit (Lay et al ., 2018; Floch et al ., 2020; Taye et al ., 2020; Wang et al ., 2020; Morales Moreirda et al ., 2021). Brassicaceae oilseed‐based rotations are common throughout the world, as demand for vegetable oil and biofuels increases (Yang et al ., 2021).…”