Abstract
The freshwater cyanobacterium Microcystis aeruginosa frequently forms toxic massive blooms and exists in an arms race with its infectious phages in aquatic natural environments, and as a result, has evolved extremely diverse and elaborate antiviral defense systems, including the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated genes (Cas) system. Here, to assess Microcystis population dynamics associated with exogenous mobile genetic elements such as phages and plasmids, we examined the temporal variation in CRISPR genotypes (CTs) by analyzing spacer sequences detected in a natural pond between June and October 2013 when a cyanobacterial bloom occurred. A total of 463,954 high-quality leader-end CRISPR sequences were obtained and the sequences containing spacers were classified into 31 previously reported CTs and 68 new CTs based on the shared order of the leader-end spacers. CT19 was the most dominant genotype (32%) among the 16 most common CTs, followed by CT52 (14%) and CT58 (9%). Spacer repertoires of CT19 showed mainly two different types; CT19origin, which was identical to the CT19 spacer repertoire of previously isolated strains, and CT19new+, which contained a new spacer at the leader-end of the CRISPR region of CT19origin, which were present in almost equal abundance, accounting for up to 99.94% of CT19 sequences. Surprisingly, we observed the spacer repertoires of the second to tenth spacers of CT19origin at the most leader-end of proto-genotype sequences of CT19origin. These were observed during the sampling in this study and our previous study at the same ecosystem in 2010 and 2011, suggesting these CTs persisted from 2011 to 2013 in spite of phage pressure. The leader-end variants were observed in other CT genotypes. These findings indicated an incomplete selective sweep of Microcystis populations. We explained the phenomenon as follow; the abundance of Microcystis varied seasonally and drastically, resulting that Microcystis populations experience a bottleneck once a year, and thereby founder effects following a bottleneck mean that older CTs have an equal chance of increasing in prevalence as the CTs generated following acquisition of newer spacers.
Highlights
Viruses infecting bacteria are ubiquitous and abundant in aquatic natural environments, with bacterial host-phage interactions shaping aquatic ecosystems (Suttle, 2005, 2007)
Bacteria exist in an arms race with the highly abundant phages (Stern and Sorek, 2011; Avrani et al, 2012), and as a result, have evolved extremely diverse and elaborate antiviral defense systems, including: (a) resistance based on variation of virus receptors, (b) immunity [e.g., the restriction-modification system and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated genes (Cas) system], and (c) dormancy induction and programmed cell death (Koonin et al, 2017)
We examined the temporal variation in CRISPR genotypes of Microcystis population by analyzing spacer sequences detected in a natural pond between June and October 2013, during a cyanobacterial bloom, using next-generation sequencing (NGS) technology
Summary
Viruses infecting bacteria (phages) are ubiquitous and abundant in aquatic natural environments, with bacterial host-phage interactions shaping aquatic ecosystems (Suttle, 2005, 2007). Several recent studies have used CRISPR-based typing to distinguish closely related strains and co-evolutionary dynamics between phage and bacteria that have shaped the species composition within bacterial populations, contributing to events such as sweeps and bottlenecks These studies have examined phage–bacterial relationships in several environments, including acid mine drainage biofilms (Andersson and Banfield, 2008; Tyson and Banfield, 2008), microbial mats in hyperthermophilic environments (Heidelberg et al, 2009; Held et al, 2010, 2013), industrial fermentation set-ups (Paez-Espino et al, 2013; Briner and Barrangou, 2014), the human oral cavity (Pride et al, 2011), and human and animal guts (Touchon and Rocha, 2010; Touchon et al, 2011). We examined the temporal variation in CRISPR genotypes of Microcystis population by analyzing spacer sequences detected in a natural pond between June and October 2013, during a cyanobacterial bloom, using next-generation sequencing (NGS) technology
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
