Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin–antitoxin system, and linkage with CRISPR-Cas system

Abstract

<i>Acetobacter</i> is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with <i>Acetobacter</i>, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in <i>Acetobacter</i>. Here, prophage prediction analysis using 148 available genomes from 34 <i>Acetobacter</i> species was carried out. In addition, the type II toxin-antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order <i>Caudovirales</i> dominated by the families <i>Siphoviridae</i> and <i>Myroviridae</i> prophages (71.4%). Notably, <i>Acetobacter</i> strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. <i>Acetobacter</i> prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in <i>Acetobacter aceti</i>, while the other <i>Acetobacter</i> species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of <i>Acetobacter</i>.