Prokaryotic CRISPR-Cas adaptive immune systems insert spacers derived from viruses and other parasitic DNA elements into CRISPR loci to provide sequence-specific immunity. This frequently results in high within-population spacer diversity, but it is unclear if and why this is important. Here we show that, as a result of this spacer diversity, viruses can no longer evolve to overcome CRISPR-Cas by point mutation, which results in rapid virus extinction. This effect arises from synergy between spacer diversity and the high specificity of infection, which greatly increases overall population resistance. We propose that the resulting short-lived nature of CRISPR-dependent bacteria-virus coevolution has provided strong selection for the evolution of sophisticated virus-encoded anti-CRISPR mechanisms.
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http://dx.doi.org/10.1038/nature17436 | DOI Listing |
Microbiome
December 2024
Faculty of Medicine, Human Microbiome Research Program, University of Helsinki, Helsinki, Finland.
Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation.
View Article and Find Full Text PDFBraz J Microbiol
December 2024
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
Orchidaceae is one of the largest plant families and stands out for its wide variety of flowers with ornamental and environmental importance. Cattleya is one of the main commercial genera, presenting a great diversity of species and hybrids that attract the attention of collectors, orchid enthusiasts, and consumers. In their natural environment, orchids associate with mycorrhizal fungi, which are responsible for providing carbon and other nutrients during seed germination.
View Article and Find Full Text PDFJ Fungi (Basel)
December 2024
Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China.
Fungi are one of the major components of the eukaryotic microbial community in marine ecosystems, playing a significant role in organic matter cycling and food web dynamics. However, the diversity and roles of fungi in marine sediments remain poorly documented. To elucidate the diversity and spatial distribution of fungal communities in the marine sediments of an estuary-coast continuum across three distinct salinity regions in Zhanjiang Bay, China, the variations in fungal diversity, abundance, community structure, and distribution in the sediments were investigated through the application of high-throughput amplicon sequencing using the internal transcribed spacer (ITS) primers.
View Article and Find Full Text PDFAppl Environ Microbiol
December 2024
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.
Unlabelled: Advances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the internal transcribed spacer (ITS) gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction.
View Article and Find Full Text PDFVavilovskii Zhurnal Genet Selektsii
November 2024
Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
During the study of algal diversity in pyroclastic deposits of the Kamchatka Peninsula, Chlorella-like green algae strains VCA-72 and VCA-93 were isolated from samples collected from along the Baydarnaya river bed on the Shiveluch volcano in 2018 and at the outlet of thermal vapors along the edge of the caldera on the southern slope of the Gorely volcano in 2020. Identification of the strains was carried out within the framework of an integrative approach using microscopic and molecular genetic methods, including preliminary taxon identification, obtaining nucleotide sequences of the small subunit and the internal transcribed spacer rRNA, reconstruction of phylogenetic trees and secondary structures of the ITS1 and ITS2 rRNA regions. On the phylogenetic tree, strain VCA-93 was clustered in the Micractinium thermotolerans species clade.
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