Targeted assemblies of <i>cas1</i> suggest CRISPR-Cas’s response to soil warming

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

doi:10.1038/s41396-020-0635-1

Cited by 9 publications

(21 citation statements)

References 53 publications

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“…Despite recent studies suggesting that CRISPR-Cas abundance varies across natural environments, such as soil 14 and the human microbiome, 15 the ecological factors that drive variation in CRISPR-Cas prevalence across natural microbial communities remained unclear. 11 Furthermore, the extent of this variation across a much wider range of environments remained unexplored.…”

Section: Resultsmentioning

confidence: 99%

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

et al. 2022

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Summary CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements. 1 Although widely distributed among prokaryotic taxa, CRISPR-Cas systems are not ubiquitous. 2 , 3 , 4 Like most defense-system genes, CRISPR-Cas are frequently lost and gained, suggesting advantages are specific to particular environmental conditions. 5 Selection from viruses is assumed to drive the acquisition and maintenance of these immune systems in nature, and both theory 6 , 7 , 8 and experiments have identified phage density and diversity as key fitness determinants. 9 , 10 However, these approaches lack the biological complexity inherent in nature. Here, we exploit metagenomic data from 324 samples across diverse ecosystems to analyze CRISPR abundance in natural environments. For each metagenome, we quantified viral abundance and diversity to test whether these contribute to CRISPR-Cas abundance across ecosystems. We find a strong positive association between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, CRISPR-Cas systems are more abundant when viral diversity is low, suggesting that such adaptive immune systems may offer limited protection when required to target a diverse viral community. CRISPR-Cas abundance also differed among environments, with environmental classification explaining roughly a quarter of the variation in CRISPR-Cas relative abundance. The relationships between CRISPR-Cas abundance, viral abundance, and viral diversity are broadly consistent across environments, providing robust evidence from natural ecosystems that supports predictions of when CRISPR is beneficial. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems.

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Section: Resultsmentioning

confidence: 99%

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

et al. 2022

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“…Despite recent studies suggesting that CRISPR-Cas abundance varies across natural environments, such as soil [15] and the human microbiome [16], the ecological factors that drive variation in CRISPR-Cas prevalence across natural microbial communities remained unclear [12]. Furthermore, the extent of this variation across a much wider range of environments remained unexplored.…”

Section: Discussionmentioning

confidence: 99%

“…Genomic evidence demonstrate that CRISPR-Cas systems are frequently acquired and lost [25, 26] and empirical studies that show that they can be mobilized through HGT [27, 28]. Notably, in a previous longitudinal study, CRISPR-Cas abundance increased through time even in phyla decreasing in abundance under soil warming conditions [15], again suggesting high mobility and positive selection for CRISPR-Cas immunity. Consistent with high rates of HGT of CRISPR-Cas, our results demonstrate that while phylogeny can influence the CRISPR-Cas repertoire, it is not the primary driver of selection in nature.…”

Section: Discussionmentioning

confidence: 99%

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High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

Meaden

Biswas

Arkhipova

et al. 2021

Preprint

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CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements. Consequently, selection from viruses and other genetic parasites is often assumed to drive the acquisition and maintenance of these immune systems in nature, but this remains untested. Here, we analyse the abundance of CRISPR arrays in natural environments using metagenomic datasets from 332 terrestrial, aquatic and host-associated ecosystems. For each metagenome we quantified viral abundance and levels of viral community diversity to test whether these variables can explain variation in CRISPR-Cas abundance across ecosystems. We find a strong positive correlation between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, we found that the CRISPR-Cas systems are more abundant when viral diversity is low. We also found differences in relative CRISPR-Cas abundance among environments, with environmental classification explaining ∼24% of variation in CRISPR-Cas abundance. However, the correlations with viral abundance and diversity are broadly consistent across diverse natural environments. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems.Significance statementNumerous studies demonstrate that CRISPR-Cas immune systems can provide defence against bacteriophage and archaeal viruses, yet little is known about the ecological conditions where CRISPR-Cas immunity is favoured. Moreover, our knowledge is largely confined to laboratory studies and it is unknown if viruses are a key selective driver of CRISPR-Cas in nature. Using metagenomic data from diverse environments we find that both viral abundance and the abundance of CRISPR-Cas immune systems correlate positively across most environments. Furthermore, CRISPR-Cas systems are more prevalent when viral diversity is low. These results extend previous theoretical work by demonstrating that viruses are a key driver of selection of CRISPR-Cas immune systems across many natural ecosystems.

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“…Microbial community is an important part of the soil ecosystem and it plays a key role in the biogeochemical processes such as the formation and transformation of soil organic matter, cycling of nutrients (Copley 2000;Wu et al 2020). Approximately 80-90% of the transformation processes in soil are mediated by microorganisms, including soil structure maintenance, organic matter dynamics, dinitrogen…”

Section: Introductionmentioning

confidence: 99%

Comparation of Bacterial and Archaea Diversity in Uncultivated and Cultivated Typical Black Soil in Northeast China

Zhao

Zhang

Shen

et al. 2021

Preprint

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Understanding the effects of tillage on the community composition and diversity of bacteria and archaea is useful for the long-term sustainable utilization of black soil. In this study, non-disturbed virgin black soil (NDBS) in the past 60 years, and the adjacent black soil under the arable land farming (DFBS) and paddy rice (PBS) for 3 years were chosen to investigate the microbial characteristics and their relationship with physical and chemical properties. The microbial diversity was investigated using 16S rRNA genes high-throughput sequencing technique and its relationship with soil physic-chemical properties was analyzed by redundancy analysis. The diversity of archaea decreased significantly after arable land farming. After conversion from arable land farming to rice paddy, the diversity of bacteria increased significantly, while the diversity of archaea increased significantly. In DFBS, the available phosphorus increased significantly, yet pH, organic matter and available potassium decreased significantly. However, the pH and available phosphorus increased significantly, organic matter and total nitrogen decreased significantly in PBS. The soil pH had the closest correlation with the microbial diversity. These indicated that tillage disturbance changed the diversity of bacteria and archaea as well as physical and chemical properties in black soil.

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

Cited by 9 publications

References 53 publications

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

Comparation of Bacterial and Archaea Diversity in Uncultivated and Cultivated Typical Black Soil in Northeast China

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