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Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis

Abstract

Microbes are by far the dominant biomass in the world’s oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13–15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.

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Fig. 1: Production and persistence of free extracellular rRNA (rRNAext) in water.
Fig. 2: Detection of cell lysis in coastal seawater as inferred from extracellular rRNA (rRNAext).
Fig. 3: Variability in the prokaryotic taxa in which lysis was detected in coastal seawater samples from the Strait of Georgia.
Fig. 4: Estimates of taxon-specific cell lysis in coastal seawater samples from the Strait of Georgia.
Fig. 5: Relative abundance of 16 S rRNAgenecell, rRNAcell, and rRNAext for different taxa and the taxon-specific cell-lysis index (CLI) for the dominant ASVs with a relative abundance of rRNAgenecell >1%.
Fig. 6: Linear regression (red line) between the relative abundance of 16 S rRNAgenecell and lysis index for individual ASVs across all samples.

Data availability

Sequencing data generated in this study have been deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers SRR14873150 to SRR14873179.

Code availability

The related codes for analyzing the taxon-specific lysis (lysis-index and lysis-rate) are included in the custom R package: tslysis (https://github.com/kevinzhongxu/tslysis).

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Acknowledgements

We thank members of the Hakai Institute for facilitating the collection of seawater samples, particularly Brian Hunt, Kate Lansley, Alex Hare and Megan Foss. We are grateful to David Caron for providing Paraphysiomonas bandaiensis for the grazing studies. Comments from the editor and two anonymous reviewers are gratefully acknowledged and were instrumental in improving the manuscript. This work was supported by grants to CAS from the Tula Foundation, the Gordon and Betty Moore Foundation (grant: GBMF#5600), a Discovery grant from the Natural Sciences and Engineering Research Council of Canada, and infrastructure awards from the Canada Foundation for Innovation and the British Columbia Knowledge Development Fund.

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KXZ designed experimental approaches, conducted experimental work, analyzed the data, wrote the initial draft of the manuscript, and oversaw subsequent versions. JFW conducted initial experimental work and edited the manuscript. AMC provided technical support throughout the project and edited the manuscript. CAS conceived the project, contributed to experimental design and data interpretation, and helped write the paper.

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Correspondence to Kevin Xu Zhong or Curtis A. Suttle.

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Zhong, K.X., Wirth, J.F., Chan, A.M. et al. Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis. ISME J 17, 105–116 (2023). https://doi.org/10.1038/s41396-022-01327-3

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