Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes

Abstract

During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31-52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes.

Keywords: coexistence; core microbiome; functional redundancy; metagenome; slime mold.

Figure 1

Six plasmodia of myxomycetes cultured on water agar media: phaneroplasmodium (a) D. squamulosum, (b) D. nigripes, (c) F. gyrosa, (d) B. melanospora, and aphanoplasmodium (e) A. cinerea, (f) M. scintillans.

Figure 2

Relative abundance of microbial communities in each plasmodium. The domain level (a) and top 15 phylum level (b) are displayed at community compositions. Phylum outside the top 15 samples was assigned as “Others”.

Figure 3

Bacterial community composition and diversity analysis of each plasmodium. (a) Hierarchical clustering analysis (weighted Unifrac UPGMA) and relative abundance of bacterial communities associated with each plasmodium and Venn diagrams show the number and abundance of shared and unique bacteria in each plasmodium at the genus level. (b) The α diversity (Chao, Shannon index, and Pielou_e) and (c) PCoA analysis using the Bray–Curtis distance metric showed the plasmodia bacterial communities’ diversity. (d) Relative abundances of the top 10 phylum levels of bacterial communities. (e) Venn diagram shows the shared and unique bacteria at the species level in each plasmodia sample. The differences were considered significant when p values < 0.05. *: p < 0.05.

Figure 4

Relative abundance of Gram-positive/Gram-negative bacteria in each plasmodium.

Figure 5

Functional analysis of plasmodia-associated bacteria. (a) A comparison of the top 25 COG functional categories in the six plasmodia. (b) Gene count and relative abundance of CAZy class categories. (c) Functional KEGG level 1 and (d) KEGG level 2 pathway descriptions, and (e) relative abundance of top 20 KEGG level 3 pathway categories.

Figure 6

Composition and functional analysis of probiotics in six myxomycetes. Relative abundance of probiotics at genus level (a) and top 25 of functional composition of probiotics (b) was exhibited in each plasmodium.