Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean

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Microbiology

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Introduction

Materials and Methods

Sample collection and environmental parameters

DNA extraction and sequencing

Sequence analysis

Data availability

Results

Environmental conditions

Community composition

Spatial and temporal distributions of SAR11 subclades

Spatial and temporal distributions of SAR11 ASVs

Frequency of SAR11 ASVs across KByT

Correlations between SAR11, picocyanobacteria, and environmental parameters

Comparison of KByT SAR11 ASVs and isolated strains

Discussion

Conclusions

Supplemental Information

Supplementary Tables S1–S9.

Table S1. Comparisons of water column parameters and cellular counts over time and space using one-way ANOVA with Tukey’s multiple comparisons test. Significance (Holm corrected p-values) are shown. Table S2. Read depth per sample. Table S3. Comparisons of read depth over time and space using one-way ANOVA with Tukey’s multiple comparisonstest. Significance (Holm corrected p-values) are shown. Table S4.Comparisons of sequencing depth across stations using one-way ANOVA with Tukey’s multiple comparisons test. Significance (Holm corrected p-values) are shown. Table S5. Detection of SAR11 ASVs across the three KByT environment types: coastal, transition, and offshore. Taxonomy was assigned in SILVA v132. SAR11 ASVs were assigned to subclades through phylogenetic placement as described in the methods. Table S6. Comparisons of the relative abundance of the top 14 most abundant orders. Significant DESeq2 normalized differences across environments are shown. Table S7. Number of SAR11 ASVs detected across KByT. Table S8: Summary of SAR11 ASVs recovered from KByT. ASVs with significant DESeq2 normalized differences across environments and seasons within each environment (C = coastal, T = transition, and O = offshore) are noted. Table S9. Summary of KByT ASVs that match isolated SAR11 strains.

DOI: 10.7717/peerj.12274/supp-1

Supplementary Figures S1–S9.

DOI: 10.7717/peerj.12274/supp-2

Additional Information and Declarations

Competing Interests

Michael S. Rappé is an Academic Editor for PeerJ.

Author Contributions

Sarah J. Tucker conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Kelle C. Freel conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Elizabeth A. Monaghan performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Clarisse E. S. Sullivan performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Oscar Ramfelt performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Yoshimi M. Rii conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Michael S. Rappé conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The data is available at NCBI SRA: PRJNA706753.

Funding

This research was supported by funding from the National Science Foundation (No. OCE-1538628) to MSR and the National Oceanic and Atmospheric Administration (NOAA) Margaret A. Davidson Fellowship (No. NA20NOS4200123) to SJT. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. 1842402 to SJT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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