Balkin, A. S. | bioRxiv Science

bioRxiv2026

Characterization of the bacterial microbiome associated with centrohelid heliozoans from aquatic environments using full-length 16S rRNA PacBio sequencing

Centrohelid heliozoans are a monophyletic group of free-living, ubiquitous, predatory protists widely distributed in aquatic and soil ecosystems. Centrohelids are known as cytotrophic protists that feed on bacteria, algae, and small unicellular eukaryotes. While algal and chloroplast symbioses have been documented in this group, their bacterial associations remain largely unexplored. In this study, we characterize the bacterial communities associated with centrohelids isolated from freshwater habitats using full-length 16S rRNA PacBio sequencing. Amplicon sequencing revealed 5 phyla, 6 classes, and 58 genera in the bacterial communities associated with seven centrohelid isolates. Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria were the most abundant classes, while Arcicella, Sphingobium, Pseudomonas, Sphingomonas, Azospirillum, Shinella, Flavobacterium, Variovorax, and Rhodococcus were the most abundant genera. Notably, Arcicella, Variovorax, Sphingobium, and Pseudomonas constituted the core microbiome. Unexpectedly, we detected bacteria known as opportunistic pathogens, providing the first evidence that centrohelids may serve as environmental reservoirs for bacteria with pathogenic potential (e.g., Acidovorax, Acinetobacter, Anaerococcus, Bosea, Corynebacterium, Escherichia, Moraxella, Mycobacterium, Prevotella, Pseudomonas, Ralstonia, and Sphingomonas). In addition, this study provides the first evidence of Rickettsiaceae associations with centrohelids. IMPORTANCEThis study reveals that centrohelid heliozoans, ubiquitous microbial predators, harbor diverse and host-specific bacterial communities. Critically, we show they can serve as environmental reservoirs for bacteria with pathogenic potential, a role previously overlooked outside of model protist groups. These findings expand our understanding of pathogen ecology, suggesting that a wider range of protists may contribute to the persistence and dispersal of opportunistic pathogens in aquatic ecosystems.

microbiology↗

bioRxiv2025

Responses of Soil Bacterial Community and Its Resistome to Short-term Exposure to Macrolide Antibiotic Macrolactin A: Metagenomic analysis

An important aspect of studying potential antibacterial biopreparations for crop protection is determining their potential negative impacts on the environment. Plant-associated Bacillus velezensis produce macrolactin A (McA), which determine effectiveness of this bacterial species against numerous human and plant pathogens. However, the effects of McA on the soil microbiome and the selection of specific antibiotic resistance genes (ARGs) among soil bacteria remain unknown. In this study, we use high-throughput sequencing-based metagenomic methods to investigate the differences in structure of the soil bacterial community and the abundance and diversity of ARGs in both McA-treated and untreated samples. The presence of high (10 mg per kg soil) and low (1 mg per kg soil) concentrations of McA induced changes in soil bacterial populations as shown by taxonomic analysis. The relative abundance of Alphaproteobacteria and Betaproteobacteria significantly increased under the McA treatments, while the relative abundance of Thermoleophilia, Rubrobacteria, Planctomycetia and Acidimicrobiia decreased. The ARG profiling results showed that both low and high doses of McA affected ARGs representation in the community. At the same time, a low dose of McA altered the representation of a larger number of ARGs (7 genes) compared to a high dose (3 genes). Overall, exposure to McA consistently altered the abundance of genes associated with resistance to elfamycin, glycopeptide, fluoroquinolone, rifampicin, and macrolide. Correlation analysis identified 185 relationships between 52 antibiotic resistance genes (ARGs) and 34 bacterial genera. Among these bacteria, Streptomyces, Baekduia, and Capillimicrobium were predicted to carry the most diverse ARGs. By assembling and annotating bacterial genomes, we identified the true hosts of ARGs. Chloroflexota were the most prevalent phylum harboring ARGs. Furthermore, profiling the soil microbiomes metabolic potential under low-dose McA revealed increased abundance of genes associated with signaling, chemotaxis, and broad-substrate drug efflux. The collectively obtained data significantly expands the understanding of the functional role of McA in the ecology of Bacillus velezensis, and at the same time provides an assessment of environmental risks associated with the use of biopreparations containing metabolites or living cells of this species bacteria.

microbiology↗