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Part of the PeerJ The Line Islands Collection

Supplemental Information

Media formulations in phenotype assay plates

Supplemental Table 1: In-house phenotypic array plate. Each stock well contains 1ml of 6X basal media (6X MOPS media, 57 mM NH4Cl, 1.5 mM NaSO4, 30 μM CaCl2, 6 mM MgSO4, 1.9M NaCl, 7.92 mM K2HPO4, 60 mM KCl, 36 μM FeCl3) and 1ml of 5X carbon substrate. The substrates are used at a final concentration of 0.2% unless specified.

DOI: 10.7287/peerj.preprints.433v1/supp-1

Orthologous groups in all the genomes

Supplemental Table 2. Orthologous groups identified in all the genomes. OG is a unique identifier; Function is the most common function annotated for all the proteins; The remaining columns identify the protein encoding genes (pegs) found in each genome or None if the gene is not present.

DOI: 10.7287/peerj.preprints.433v1/supp-2

2013 Southern Line Islands Research Expedition

Supplemental Figure 1: Expedition route of the 2013 Southern Line Island Expedition. The expedition left Papeete Harbor and circumnavigated the Southern Line Islands in a clockwise direction.

DOI: 10.7287/peerj.preprints.433v1/supp-3

Sampling the reefs

Supplemental Figure 2: Examples of sampling surface for bacterial isolates. VRT35 and VRT38 were isolated from coral surfaces, while VRT37 and VRT41 were isolated from algae surfaces.

DOI: 10.7287/peerj.preprints.433v1/supp-4

Number of bases sequenced and number of contigs generated

Supplemental Figure 3. Number of bases sequenced and number of contigs generated. The best-fit power regression of the data (shown with a gray line) has the equation [number of contigs] = 3.87 * 1010 [base piars sequenced]-0.95 with an R2 of 0.667.

DOI: 10.7287/peerj.preprints.433v1/supp-5

Growth curves in 48 different media showing growth in some wells

Supplemental Figure 4: Growth curve of bacterial isolates in 48 different carbon sources indicated in Supplementary Table 1.

DOI: 10.7287/peerj.preprints.433v1/supp-6

Heat map showing growth characteristics of all the isolates

Supplemental Figure 5: Heatmap showing the growth characteristics of each bacterial isolates from the 2013 Southern Line Island expedition in 48 different carbon sources.

DOI: 10.7287/peerj.preprints.433v1/supp-7

Negative controls don't grow

Supplemental Figure 6: Growth curve of negative controls and filtered seawater-only samples in 48 different carbon sources indicated in Supplementary Table 1.

DOI: 10.7287/peerj.preprints.433v1/supp-8

There is no correlation between genetic and physical distance

Supplemental Fig 7. Correlation between physical distance and genetic distance in the microbial species purified on the Line Islands.

DOI: 10.7287/peerj.preprints.433v1/supp-9

Additional Information

Competing Interests

Timothy Harkins, Clarence Lee, and Warren Tom are employees of Life Technologies, Inc. and that Mark JA Vermeij is an employee of the Caribbean Research and Management of Biodiversity (CARMABI).

Author Contributions

Yan Wei Lim conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Daniel A Cuevas analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Genivaldo Gueiros Z. Silva analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Kristen Aguinaldo analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Elizabeth Dinsdale contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Andreas F Haas performed the experiments, analyzed the data, reviewed drafts of the paper.

Mark Hatay contributed reagents/materials/analysis tools, prepared figures and/or tables, reviewed drafts of the paper.

Savannah E Sanchez contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Linda W. Kelly analyzed the data, reviewed drafts of the paper.

Bas E. Dutilh analyzed the data, reviewed drafts of the paper.

Timothy T. Harkins contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Clarence C Lee contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Warren Tom contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Stuart A Sandin reviewed drafts of the paper, organized the field expedition, permits, and logistics.

Jennifer Smith reviewed drafts of the paper, organized the field expedition, permits, and logistics.

Brian Zgliczynski reviewed drafts of the paper, organized the field expedition, permits, and logistics.

Mark JA Vermeij performed the experiments, reviewed drafts of the paper.

Forest Rohwer conceived and designed the experiments, performed the experiments, reviewed drafts of the paper.

Robert Edwards conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

All samples were collected on SCUBA and under the Scientific Research Permit 021/13 issued by the Environment and Conservation Division of the Republic of Kiribati.

Grant Disclosures

The following grant information was disclosed by the authors:

NSF DEB-1046413, NSF CNS-1305112, NSF MCB-1330800

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All sequences are in NCBI Bioproject PRJNA253472

Individual sequences:

NCBI BioSample Database

SAMN02904893

SAMN02904892

SAMN02870694

SAMN02870695

SAMN02870696

SAMN02870697

SAMN02870670

SAMN02870717

SAMN02870718

SAMN02870712

SAMN02870698

SAMN02870713

SAMN02870714

SAMN02870715

SAMN02870699

SAMN02870716

SAMN02870706

SAMN02870707

SAMN02870710

SAMN02870700

SAMN02870711

SAMN02870701

SAMN02870702

SAMN02870703

SAMN02870704

SAMN02870708

SAMN02870705

SAMN02870709

Data Deposition

The following information was supplied regarding the deposition of related data:

We will deposit figures in FigShare

Funding

This work is partially supported by NSF Dimensions Grant (DEB-1046413; Edwards and Rohwer). This project was also funded in part by the Gordon and Betty Moore Foundation through Grant GBMF-3781 to Rohwer. Additional funding for Yanwei Lim was provided by the Canadian Institute for Advanced Research (CIFAR; IMB-ROHW-141679). Additional funding for Edwards was provided by NSF grants CNS-1305112, and MCB-1330800. Dutilh was supported by an award from CAPES/BRASIL. The SDSU Vice President of Research, Director's Office of Scripps Institution of Oceanography, Moore Family Foundation, and several private donors provided cruise support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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