Genomic characterization of antifungal Acinetobacter bacteria isolated from the skin of the frogs Agalychnis callidryas and Craugastor fitzingeri

Abstract

Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. Five isolates belonged to A. pittii, A. radioresistens, or A. modestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

“…Genomic analysis of bacteria isolated from amphibian skin revealed the presence of genes linked to biosynthesis of various metabolites that could be linked to host protection against Bd and host-microbiome interactions [93,94,116]. Specifically, genes linked to AF traits have been linked to the biosynthesis of chitinolytic enzymes [22], and secondary metabolites such as ribosomal and non-ribosomal peptides (RiPP and NRPS), aryl-polyenes, polyketides, or bacteriocins [58,93,94].…”

“…To evaluate if genes linked to potential antifungal functions differed across seasons, elevations/sites and Bd infection status, a PERMANOVA test was used comparing abundances of genes linked to bacterial communication and competition traits (BCC: biofilm formation, quorum sensing and secretion systems) and potential antifungal functions (AF: secondary metabolite and chitinolytic enzyme biosynthesis). Selection of these gene categories was based on published literature suggesting that these functions may contribute to host protection against Bd [22,40,53,58,93,94].…”

Amphibian skin bacteria display antifungal activity and induce plant defense mechanisms against Botrytis cinerea

“…Antifungal activity assay for the selected bacteria against B. cinerea Bacteria were previously identified by Rebollar et al (2019). The bacteria C26G and C32I were recently described as new species of the Acinetobacter genus (Cevallos et al, 2022), while C23F was identified at the family level as Enterobacteraceae through 16S rRNA sequencing (Rebollar et al, 2018). All bacteria isolates were initially screened for their antifungal activity against the pathogen B. cinerea by the direct confrontation assay.…”

Proposal for Acinetobacter higginsii sp. nov. to accommodate organisms of human clinical origin previously classified as Acinetobacter genomic species 16

“…This clade currently includes 14 species with correct names and five provisional taxa with not yet defined nomenclatural status (Table S1, ) [1]. In addition, several taxonomically unique strains belonging to the clade were reported [4–6]. The haemolytic clade consists of several subclades, which markedly differ from each other in phenotypic and genomic features.…”

“…1) [1]. In addition, several taxonomically unique strains belonging to the clade were reported [4][5][6]. The haemolytic clade consists of several subclades, which markedly differ from each other in phenotypic and genomic features.…”