Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches

Abstract

One of the key factors affecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two different approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specific. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less affected by agricultural practices.

Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth

“…From these projects, the abundant genera found concerning wheat endophytes were Bacillus, Stenotrophomonas, Pseudomonas, Acinetobacter, Enterobacter, Clostridium, and Xanthomonas. The previous experiment, carried out by Tkalec et al (2022), supported our findings, where they observed abundance of Bacillus species in their samples. The bacterial genera Clostridium and Xanthomonas were excluded from community formation due to their pathogenic nature for plants and animals.…”

The seed microbiomes of staple food crops

“…As shown in Figure 4A,B, Curtobacterium, Bacillus and Pantoea are the most abundant bacterial genera, while Aureobasidium, Fusarium and Alternaria are the richest in fungal genera. However, a bit different from the previous reports, it was found that wheat and maize are mainly composed of three bacterial genera (Bacillus, Paenibacillus Curtobactreium) and one fungal, Aspergillus, based on both sequencing and culturing techniques (Tkalec et al, 2022). In addition, wheat and maize share only less than 10% microbial population under both conventional and organic farming systems.…”

Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms

“…Generally, the relative content was bacteria > fungi > protozoa > viruses, but in maize kernels and roots, the relative content of fungi exceeded that of bacteria. In general, numerous studies have shown that bacteria are the predominant of all microorganisms [45][46][47], but the results of the new analysis strategy showed the composition of various types of microorganisms, from which it can be seen that eukaryotic microorganisms, including fungi and protozoa, sometimes dominate in specific tissues. In addition, protozoa are generally not a hot spot for research on plant endophytic microorganisms; however, in this study, we note that the relative content of protozoa should not be neglected, as they may also play an important role in promoting plant growth and other aspects.…”