Diversity of bacterial communities in the plasmodia of myxomycetes

Abstract

Background: Myxomycetes are a group of eukaryotes belonging to Amoebozoa, which are characterized by a distinctive life cycle, including the plasmodium stage and fruit body stage. Plasmodia are all found to be associated with bacteria. However, the information about bacteria diversity and composition in different plasmodia was limited. Therefore, this study aimed to investigate the bacterial diversity of plasmodia from different myxomycetes species and reveal the potential function of plasmodia-associated bacterial communities.

Results: The bacterial communities associated with the plasmodia of six myxomycetes (Didymium iridis, Didymium squamulosum, Diderma hemisphaericum, Lepidoderma tigrinum, Fuligo leviderma, and Physarum melleum) were identified by 16S rRNA amplicon sequencing. The six plasmodia harbored 38 to 52 bacterial operational taxonomic units (OTUs) that belonged to 7 phyla, 16 classes, 23 orders, 40 families, and 53 genera. The dominant phyla were Bacteroidetes, Firmicutes, and Proteobacteria. Most OTUs were shared among the six myxomycetes, while unique bacteria in each species only accounted for a tiny proportion of the total OTUs.

Conclusions: Although each of the six myxomycetes plasmodia had different bacterial community compositions, a high similarity was observed in the plasmodia-associated bacterial communities' functional composition. The high enrichment for gram-negative (> 90%) and aerobic (> 99%) bacteria in plasmodia suggest that myxomycetes may positively recruit certain kinds of bacteria from the surrounding environment.

Keywords: 16S rRNA; Amplicon sequencing; Bacteria; Slime mold.

Fig. 1

Six plasmodia cultured on oat—agar media. a Didymium iridis (Ditmar) Fr.; b Didymium squamulosum (Alb. & Schwein.) Fr.; c Diderma hemisphaericum (Bull.) Hornem.; d Lepidoderma tigrinum (Schrad.) Rostaf.; e Fuligo leviderma H. Neubert, Nowotny & K. Baumann; f Physarum melleum (Berk. & Broome) Massee

Fig. 2

Bacterial communities associated with plasmodia. a Phylogenetic analysis of bacterial communities associated with six myxomycetes at the genus level. A neighbor-joining tree exhibit the bacterial genera (relative abundance above 0.1%) detected in this study. Colored bars represent the relative abundance of each genus in the six plasmodia. b Hierarchical clustering analysis (Weighted Unifrac UPGMA) of bacterial communities associated with each plasmodium and relative abundance of bacteria at the OTU level

Fig. 3

Venn diagrams of overlapping OTUs. Colored bars represented the relative abundance of common and unique OTUs

Fig. 4

Phenotypes and function of bacterial communities predicted in 6 myxomycetes. a Gram bacterial classification predicted by BugBase. b Oxygen utilization predicted by BugBase. c Top 30 enriched KEGG function at level 3 prediction of bacterial communities associated with six myxomycetes by PICRUSt2