Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin

Abstract

Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn 2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.

Distribution and ecology of the generalist lactic acid bacterium Carnobacterium maltaromaticum in different freshwater habitats: Metabolic and antagonistic abilities

“…Structured habitats may support selection for bactericinogenic bacteria (Chao & Levin, 1981). Other firmicutes can be present in higher proportions in freshwater sediments (Costa et al, 2022) that are examples of such structured habitats and therefore a more likely scenario for selection for antagonistic activity. Animals represent another example on structured habitats and indeed C. maltaromaticum has been noted as an important element of the microbial communities of amphibians and freshwater fish as well as insects, including various moths and a species of ant associated with sphagnum‐associated habitats such as the habitat III locations included in this study (Iskandar et al, 2017; Leisner et al, 2007; Liu et al, 2021; Pastorino et al, 2021; Pastorino et al, 2023; Scarparo et al, 2021; Shannon et al, 2001; Xia et al, 2017; Yu et al, 2008).…”

“…The latter situation is relevant in, for example, fermented foods but is less likely to play a role in freshwater environments, especially as LAB are generally only present in low numbers compared to other heterotrophic bacteria (Leisner et al, 2008; Yanagida et al, 2007, this study; Figure 2A). LAB antagonistic activities due to bacteriocins have been well studied in food systems (Leisner & Haaber, 2012; Martinenghi & Leisner, 2022), whereas this is not so for the freshwater environment, although a recent study demonstrated a divergicin‐encoding gene, associated with C. divergens , among other bacteriocin‐encoding genes present in hydroelectric power plant water (Costa et al, 2022). For this reason, we examined the intra‐specific and interspecific antagonistic activities of freshwater isolates of C. maltaromaticum and explored to which degree these activities were due to bacteriocins.…”