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

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

doi:10.1038/s41396-020-0635-1

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

Journal Article · Fri Mar 27 00:00:00 EDT 2020 · The ISME Journal

DOI:https://doi.org/10.1038/s41396-020-0635-1· OSTI ID:1619812

; Chai, Benli; Cole, James R.; Gunturu, Santosh K.; Guo, Xue; Tian, Renmao; ; ; Tiedje, James M.

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.

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Research Organization:: Michigan State Univ., East Lansing, MI (United States); Univ. of Oklahoma, Norman, OK (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: FG02-99ER62848; SC0010715

OSTI ID:: 1619812

Alternate ID(s):: OSTI ID: 1800980

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 7 Vol. 14; ISSN 1751-7362

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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