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Dynamics between the bacterial immune system (CRISPR) and viruses in the Baltic Sea

Hultgren, Marcus LU (2018) KBKM05 20181
Pure and Applied Biochemistry
Computational Chemistry
Abstract
Bacteria play a major role in biogeochemical cycles in the ocean. Bacteriophages are estimated to cause the deaths of more than a fifth of all marine bacteria every day and the dynamic between bacteria and virus therefore have huge ecological impact. CRISPR-Cas systems work as an adaptive immune system for bacteria that protect them against viruses. Spacers acquired from viral sequences can make the bacteria immune to any virus carrying the sequence. Samples from the Baltic Sea were taken in a metagenomic timeseries spanning over the period 2012-2015. Spacers from CRISPR samples were aligned with Bowtie2 against the virus samples. By studying the number of matches that occurred between the different CRISPR and virus samples, we analysed... (More)
Bacteria play a major role in biogeochemical cycles in the ocean. Bacteriophages are estimated to cause the deaths of more than a fifth of all marine bacteria every day and the dynamic between bacteria and virus therefore have huge ecological impact. CRISPR-Cas systems work as an adaptive immune system for bacteria that protect them against viruses. Spacers acquired from viral sequences can make the bacteria immune to any virus carrying the sequence. Samples from the Baltic Sea were taken in a metagenomic timeseries spanning over the period 2012-2015. Spacers from CRISPR samples were aligned with Bowtie2 against the virus samples. By studying the number of matches that occurred between the different CRISPR and virus samples, we analysed the effects that seasonal and temporal variation has on the match frequency. Both seasonal and temporal variations were found to have significance, demonstrating that the abundance of viruses is connected to seasonal dynamics, likely linked to the host population. The temporal variation shows that the effectiveness of individual spacers decreases continuously, either due to the fast mutation rate of viruses, or changes in the virus population. Blasting the direct repeat sequences against a database consisting of compiled bins from metagenome-assembled genomes and the Refseq genome data base enabled the annotation of a fourth of the CRISPRs that matched to viral contigs. Visualisation of CRISPR-virus networks resulted in the finding of virus contigs that connected bacteria from different genus, order and phyla which suggests that there could exist viruses that are able to target a diverse set of hosts. (Less)
Popular Abstract (Swedish)
En ml vatten från havsvatten innehåller ungefär 1 miljon bakterier och 10 miljoner virus. Prover från Östersjön har undersökts genom dataanalys för att studera dynamiken mellan bakteriers adaptiva immunförsvar – CRISPR - och virus.
Please use this url to cite or link to this publication:
author
Hultgren, Marcus LU
supervisor
organization
course
KBKM05 20181
year
type
H2 - Master's Degree (Two Years)
subject
keywords
Metagenomics, Bioinformatics, CRISPR, Virus, Bacteria, Baltic Sea, Applied Biotechnology
language
English
id
8951072
date added to LUP
2022-06-30 10:16:29
date last changed
2022-06-30 10:16:29
@misc{8951072,
  abstract     = {{Bacteria play a major role in biogeochemical cycles in the ocean. Bacteriophages are estimated to cause the deaths of more than a fifth of all marine bacteria every day and the dynamic between bacteria and virus therefore have huge ecological impact. CRISPR-Cas systems work as an adaptive immune system for bacteria that protect them against viruses. Spacers acquired from viral sequences can make the bacteria immune to any virus carrying the sequence. Samples from the Baltic Sea were taken in a metagenomic timeseries spanning over the period 2012-2015. Spacers from CRISPR samples were aligned with Bowtie2 against the virus samples. By studying the number of matches that occurred between the different CRISPR and virus samples, we analysed the effects that seasonal and temporal variation has on the match frequency. Both seasonal and temporal variations were found to have significance, demonstrating that the abundance of viruses is connected to seasonal dynamics, likely linked to the host population. The temporal variation shows that the effectiveness of individual spacers decreases continuously, either due to the fast mutation rate of viruses, or changes in the virus population. Blasting the direct repeat sequences against a database consisting of compiled bins from metagenome-assembled genomes and the Refseq genome data base enabled the annotation of a fourth of the CRISPRs that matched to viral contigs. Visualisation of CRISPR-virus networks resulted in the finding of virus contigs that connected bacteria from different genus, order and phyla which suggests that there could exist viruses that are able to target a diverse set of hosts.}},
  author       = {{Hultgren, Marcus}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Dynamics between the bacterial immune system (CRISPR) and viruses in the Baltic Sea}},
  year         = {{2018}},
}