Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates

• Published in: Applied and environmental microbiology 2023-07, Vol.89 (7), p.e0017723-e0017723
• Main Authors: Kosmopoulos, James C, Campbell, Danielle E, Whitaker, Rachel J, Wilbanks, Elizabeth G
• Format: Article
• Language: English
• Subjects: Aggregates; Bacteria; BASIC BIOLOGICAL SCIENCES; Berries; Biotechnology & Applied Microbiology; Coevolution; Community structure; Conserved sequence; Consortia; CRISPR; Evolution; Evolutionary and Genomic Microbiology; Fruits; Gene transfer; Horizontal transfer; Metagenomics; Microbial activity; Microbiology; Microorganisms; Natural environment; Nucleotides; Phages; Salt marshes; Symbionts; Viruses
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.00177-23

Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, sp. PB-SRB1, sp. PB-PSB1, and sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, a