Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

Anderson, R.; Brazelton, William J.; Baross, John A.

doi:10.1111/j.1574-6941.2011.01090.x

Cited by 116 publications

(117 citation statements)

References 62 publications

(85 reference statements)

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“…3). Consistent with the idea that the CRISPR system is better when the risk of infection is low, thermophiles tend to have more and longer CRISPRs (147,148) and have lower host and parasite population densities (149). Similar effects are expected in the context of other immune mechanisms that have inducible costs.…”

Section: Costs Of Resistance Can Help To Explain Diversity In Immune supporting

confidence: 67%

Evolutionary Ecology of Prokaryotic Immune Mechanisms

Houte

Buckling

Westra

2016

Microbiol Mol Biol Rev

209

177

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SUMMARYBacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.

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Section: Costs Of Resistance Can Help To Explain Diversity In Immune supporting

confidence: 67%

Evolutionary Ecology of Prokaryotic Immune Mechanisms

Houte

Buckling

Westra

2016

Microbiol Mol Biol Rev

209

177

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“…CRISPR systems potentially provide haloarchaea with a dynamic means to respond and defend against specific haloarchaeoviruses (for example, Andersson and Banfield, 2008;Tyson and Banfield, 2008;Heidelberg et al, 2009;Anderson et al, 2010;Held et al, 2010;Emerson et al, 2013;Maier et al, 2013;Vestergaard et al, 2014). Spacers are incorporated into loci between short direct repeat sequences and, along with the CRISPR-associated (Cas) proteins, are characteristic of the host in which they evolved.…”

Section: Introductionmentioning

confidence: 99%

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

et al. 2015

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Despite knowledge that viruses are abundant in natural ecosystems, there is limited understanding of which viruses infect which hosts, and how both hosts and viruses respond to those interactions—interactions that ultimately shape community structure and dynamics. In Deep Lake, Antarctica, intergenera gene exchange occurs rampantly within the low complexity, haloarchaea-dominated community, strongly balanced by distinctions in niche adaptation which maintain sympatric speciation. By performing metaproteomics for the first time on haloarchaea, genomic variation of S-layer, archaella and other cell surface proteins was linked to mechanisms of infection evasion. CRISPR defense systems were found to be active, with haloarchaea responding to at least eight distinct types of viruses, including those infecting between genera. The role of BREX systems in defending against viruses was also examined. Although evasion and defense were evident, both hosts and viruses also may benefit from viruses carrying and expressing host genes, thereby potentially enhancing genetic variation and phenotypic differences within populations. The data point to a complex inter-play leading to a dynamic optimization of host–virus interactions. This comprehensive overview was achieved only through the integration of results from metaproteomics, genomics and metagenomics.

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“…Of three provirus-matching spacers in Aca_3, two spacers showed synonymous and nonsynonymous substitutions compared with their corresponding putative protospacers in proviruses ( Table 4), indicating that A. camini interacted with viruses that were closely related to APSV1 and APOV1. All CRISPR spacers did not show a significant match with any other nucleotide sequences in the nr database or viral metagenomes from Yellowstone hot springs (21) and the Juan de Fuca ridge (22) other than the APSV1 and APOV1 genomes. It is noteworthy that none of the CRISPR spacers matched the nonorthologous genes of Aeropyrum spp., which are extrachromosomal elements in most cases (described below).…”

Section: Resultsmentioning

confidence: 99%

“…The spacer sequences were clustered by using CD-HIT-EST (20), with a local sequence identity threshold of 90%, an alignment coverage threshold for a shorter sequence of 60%, and a word size set at 7. Two available viral metagenomes from Yellowstone hot springs (21) and from the Juan de Fuca ridge (22) were retrieved from the GenBank trace archive and from the CAMERA database (23), respectively. A similarity search of spacer sequences was performed against the NCBI nonredundant (nr) database and the viral metagenomes by using BLASTN (24), with an E value threshold of 10 Ϫ5 and a word size set at 7.…”

Section: Methodsmentioning

confidence: 99%

Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum

Daifuku¹,

Yoshida²,

Kitamura³

et al. 2013

Appl Environ Microbiol

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The increasing number of genome sequences of archaea and bacteria show their adaptation to different environmental conditions at the genomic level. Aeropyrum spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were a small genome size, a high GC content, and a large portion of orthologous genes (86 to 88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the entire-genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A. pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini CRISPR showed significant matches with protospacers of the two proviruses infecting A. pernix, indicating that A. camini interacted with viruses closely related to APSV1 and APOV1. Furthermore, a significant fraction of the nonorthologous genes (41 to 45%) were proviral genes or ORFans probably originating from viruses. Although the genomes of A. camini and A. pernix were conserved, we observed nonsynteny that was attributed primarily to virus-related elements. Our findings indicated that the genomic diversification of Aeropyrum spp. is substantially caused by viruses. Between closely related organisms, gene repertoires and genome organizations differ depending on the ecological characteristics of each habitat. For example, whole-genomic comparisons of the cyanobacterial Prochlorococcus spp., with physiological features relevant to the different ecological niches within a stratified oceanic water column, show gross signatures of this niche differentiation (1). The members of the anaerobic hyperthermophilic archaeal genus Pyrococcus adapt to abiotic and biotic environmental conditions through positive gene selection (2). Although genomes of temperate coastal SAR11 isolates are highly conserved in the core genome common to all strains (3) and show synteny (the conservation of DNA sequence and gene order) (4), variations exist among genes for phosphorus metabolism, glycolysis, and C 1 metabolism. This suggests that adaptive specialization in nutrient resource utilization is important for niche partitioning (5).Aeropyrum species are heterotrophic, aerobic, neutrophilic, and hyperthermophilic archaea. The two currently known species, Aeropyrum pernix and Aeropyrum camini, were isolated from geographically distinct locations. The type strain of the type species, A. pernix K1, was isolated from a coastal solfataric vent on Kodakara-Jima Island in southwes...

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Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage

Cited by 116 publications

References 62 publications

Evolutionary Ecology of Prokaryotic Immune Mechanisms

Evolutionary Ecology of Prokaryotic Immune Mechanisms

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation

Variation of the Virus-Related Elements within Syntenic Genomes of the Hyperthermophilic Archaeon Aeropyrum

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