Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Ruonan Wu, Benli Chai, James R. Cole, Santosh K. Gunturu, Xue Guo, Renmao Tian, Ji Dong Gu, Jizhong Zhou, James M. Tiedje*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.

Original languageEnglish
Pages (from-to)1651-1662
Number of pages12
JournalISME Journal
Volume14
Issue number7
DOIs
StatePublished - 1 Jul 2020
Externally publishedYes

Fingerprint Dive into the research topics of 'Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming'. Together they form a unique fingerprint.

Cite this