Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes

University of Hyderabad, India
PLoS ONE (Impact Factor: 3.23). 02/2009; 4(1):e4169. DOI: 10.1371/journal.pone.0004169
Source: PubMed


CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B') as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

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Available from: Devaki Bhaya, Apr 20, 2015
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    • "The presence of phage genes and CRISPR regions in the JS1T genome suggests the epilithic biofilm hosts viruses and bacteriophage that may pose threats to the bacteria. This is an interesting observation because CRISPR regions have also been reported in microbes in hot-spring photoautotrophic mats in volcanically active Yellowstone National Park and this may indicate higher virus activities in geothermally active areas [18]. "
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    ABSTRACT: The ancestor of Gloeobacter violaceus PCC 7421(T) is believed to have diverged from that of all known cyanobacteria before the evolution of thylakoid membranes and plant plastids. The long and largely independent evolutionary history of G. violaceus presents an organism retaining ancestral features of early oxygenic photoautotrophs, and in whom cyanobacteria evolution can be investigated. No other Gloeobacter species has been described since the genus was established in 1974 (Rippka et al., Arch Microbiol 100:435). Gloeobacter affiliated ribosomal gene sequences have been reported in environmental DNA libraries, but only the type strain's genome has been sequenced. However, we report here the cultivation of a new Gloeobacter species, G. kilaueensis JS1(T), from an epilithic biofilm in a lava cave in Kīlauea Caldera, Hawai'i. The strain's genome was sequenced from an enriched culture resembling a low-complexity metagenomic sample, using 9 kb paired-end 454 pyrosequences and 400 bp paired-end Illumina reads. The JS1(T) and G. violaceus PCC 7421(T) genomes have little gene synteny despite sharing 2842 orthologous genes; comparing the genomes shows they do not belong to the same species. Our results support establishing a new species to accommodate JS1(T), for which we propose the name Gloeobacter kilaueensis sp. nov. Strain JS1(T) has been deposited in the American Type Culture Collection (BAA-2537), the Scottish Marine Institute's Culture Collection of Algae and Protozoa (CCAP 1431/1), and the Belgian Coordinated Collections of Microorganisms (ULC0316). The G. kilaueensis holotype has been deposited in the Algal Collection of the US National Herbarium (US# 217948). The JS1(T) genome sequence has been deposited in GenBank under accession number CP003587. The G+C content of the genome is 60.54 mol%. The complete genome sequence of G. kilaueensis JS1(T) may further understanding of cyanobacteria evolution, and the shift from anoxygenic to oxygenic photosynthesis.
    PLoS ONE 10/2013; 8(10):e76376. DOI:10.1371/journal.pone.0076376 · 3.23 Impact Factor
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    • "Of the relatively few metagenomic analyses of virus-host dynamics that have been reported, several have considered the clustered regularly interspaced short palindromic repeat (CRISPR) system, which provides an opportunity to study hosts' responses to viral predation and to link viruses to hosts [8–12]. The CRISPR system is a genomic region in nearly all archaea and some bacteria, and CRISPRs (at least in all systems that have been biochemically characterized to date) have been shown to confer adaptive immunity to viruses and/or other mobile genetic elements through nucleotide sequence identity between the host CRISPR system and invading nucleic acids [13, 14]. "
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    ABSTRACT: The study of natural archaeal assemblages requires community context, namely, a concurrent assessment of the dynamics of archaeal, bacterial, and viral populations. Here, we use filter size-resolved metagenomic analyses to report the dynamics of 101 archaeal and bacterial OTUs and 140 viral populations across 17 samples collected over different timescales from 2007-2010 from Australian hypersaline Lake Tyrrell (LT). All samples were dominated by Archaea (75-95%). Archaeal, bacterial, and viral populations were found to be dynamic on timescales of months to years, and different viral assemblages were present in planktonic, relative to host-associated (active and provirus) size fractions. Analyses of clustered regularly interspaced short palindromic repeat (CRISPR) regions indicate that both rare and abundant viruses were targeted, primarily by lower abundance hosts. Although very few spacers had hits to the NCBI nr database or to the 140 LT viral populations, 21% had hits to unassembled LT viral concentrate reads. This suggests local adaptation to LT-specific viruses and/or undersampling of haloviral assemblages in public databases, along with successful CRISPR-mediated maintenance of viral populations at abundances low enough to preclude genomic assembly. This is the first metagenomic report evaluating widespread archaeal dynamics at the population level on short timescales in a hypersaline system.
    Archaea 06/2013; 2013(2):370871. DOI:10.1155/2013/370871 · 2.71 Impact Factor
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    • "What we know about CRISPR function empirically derives largely from the study of S. thermophilus (Deveau et al. 2008; Horvath et al. 2008). However, CRISPR-like mechanisms have been reported in a wide variety of hosts, including E. coli (Westra et al. 2010), acid mine drainage bacteria (Andersson and Banfield 2008), thermophiles such as Sulfolobus islandicus (Held et al. 2010), and microbial mat bacteria (Heidelberg et al. 2009), to name just a few of a growing list of examples. As such, this (or any other) model cannot be considered comprehensive. "
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    ABSTRACT: The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
    Evolution 07/2012; 66(7):2015-29. DOI:10.1111/j.1558-5646.2012.01595.x · 4.61 Impact Factor
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