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Small tropical islands with dense human population: Differences in water quality of near-shore waters are associated with distinct bacterial communities

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Small tropical islands with dense human population: Differences in water quality of near-shore waters are associated with distinct bacterial communities https://t.co/On4696PC5n
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Supplemental Information

Raw R-code for the submitted analyses

This is the provided raw code for the conducted bioinformatics analyses in R.

DOI: 10.7287/peerj.preprints.26553v1/supp-1

Bacterial diversity based on the inverse Simpson index at the inhabited and uninhabited island and its correlation with water quality parameters

A+B: Bacterial diversity of the free-living fraction of the water column (> 0.2 µm; FL). C+D: Bacterial diversity of the particle-attached fraction of the water column (> 3 µm; PA). E+F: Bacterial diversity in the reef sediment (SED). A+C+E: Individual diversity estimates and their median (horizontal line) of the bacterial communities at each island. B+D+F: Correlation coefficients based on Spearman-rank correlations with error bars depicting 95% confidence intervals. Inverse Simpson Indices were calculated based on repeatedly randomly rarefying the data set to the minimum library size (964 sequences). NOx:nitrite/nitrate, PO43‑:phosphate, Si: silicate, Chl a: Chlorophyll a, DOC: dissolved organic carbon, TEP: transparent exopolymer particles.

DOI: 10.7287/peerj.preprints.26553v1/supp-2

Rarefaction analysis of alpha diversity indices of bacterial communities at the inhabited and uninhabited island

Rarefaction analysis of alpha diversity indices of bacterial communities at the inhabited and uninhabited island for sequencing depths of 0 to 20000 sequences using the R packageiNEXT. (A+B) Bacterial diversity of the free-living fraction of the water column (> 0.2 µm; FL). (C+D) Bacterial diversity of the particle-attached fraction of the water column (> 3 µm; PA). (E+F) Bacterial diversity in the reef sediment (SED). (A+C+E) Number of OTUs (Hill number q = 0). (B+D+F) Inverse Simpson Index (Hill number q = 2). Solid lines: interpolated diversity indices, dashed lines: extrapolated diversity indices, shaded area: confidence interval of diversity estimates.

DOI: 10.7287/peerj.preprints.26553v1/supp-3

Composition and dissimilarity of bacterial communities at the inhabited and uninhabited island

(A) Cluster diagram based on Bray-Curtis dissimilarity coefficients constructed using average linkage. (B) Class-level taxonomic composition of the bacterial communities. FL: Free-living bacterial communities of the water column (> 0.2 µm), PA: Particle-attached bacterial communities of the water column (> 3 µm), SED: Bacterial communities in reef sediments.

DOI: 10.7287/peerj.preprints.26553v1/supp-4

Heatmap of centered log ratio (clr)-transformed sequence counts of OTUs best suited to differentiate bacterial communities between the inhabited and uninhabited island based on random forest analysis

Red colors indicate an enrichment of an OTU compared to the average sequence contribution of all OTUs in a sample, whereas blue colors indicate depletion. For each OTU, its class-level affiliation, last classified taxonomic rank, and sequence number are provided. FL: Free-living bacterial communities of the water column (> 0.2 µm), PA: Particle-attached bacterial communities of the water column (> 3 µm), SED: Bacterial communities in reef sediments.

DOI: 10.7287/peerj.preprints.26553v1/supp-5

Heatmap of centered log ratio (clr)-transformed sequence counts of potentially pathogenic OTUs identified in the inhabited and uninhabited island based on random forest analysis

Red colors indicate an enrichment of an OTU compared to the average sequence contribution of all OTUs in a sample, whereas blue colors indicate depletion. For each OTU, its genus-level affiliation and sequence number are provided. FL: Free-living bacterial communities of the water column (> 0.2 µm), PA: Particle-attached bacterial communities of the water column (> 3 µm), SED: Bacterial communities in reef sediments.

DOI: 10.7287/peerj.preprints.26553v1/supp-6

Summary of the water quality parameters at the inhabited (BL: Barrang Lompo) and the uninhabited island (KK: Kodinggareng Keke)

NOx-: nitrite/nitrate, PO43-: phosphate, Si: silicate, Chl a: Chlorophyll a, DOC: dissolved organic carbon, TEP: transparent exopolymer particles, N: number of replicates, SD: standard deviation, SEM: standard error of the mean.

DOI: 10.7287/peerj.preprints.26553v1/supp-7

List of eigenvectors of the individual water quality parameters contributing to the principal components (PC) of Fig. 3

NOx-: nitrite/nitrate, PO43-: phosphate, Si: silicate, Chl a: Chlorophyll a, DOC: dissolved organic carbon, TEP: transparent exopolymer particles.

DOI: 10.7287/peerj.preprints.26553v1/supp-8

Number of generated (raw) and quality-checked (final) sequences produced from bacterial communities of the free-living and particle-attached fraction of the water column and reef sediment at the inhabited (BL: Barrang Lompo) and the uninhabited island (KK

OTU number (nOTU) and Inverse Simpson diversity index (invS) were calculated based on the complete data set as well as repeatedly randomly rarefying the data set to the minimum library size (964 sequences).

DOI: 10.7287/peerj.preprints.26553v1/supp-9

Performance of the random forest analysis to predict the inhabitation status of the islands based on their microbial communities. Each model was run with 10001 trees

Performance of the random forest analysis to predict the inhabitation status of the islands based on their microbial communities. Each model was run with 10001 trees.

DOI: 10.7287/peerj.preprints.26553v1/supp-10

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

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

Christiane Hassenrueck analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Pia Kegler performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Tim C Jennerjahn conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Muhammad Lukman conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, assisted in obtaining the necessary research permits.

Jamaluddin Jompa conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, assisted in obtaining the necessary research permits.

Astrid Gärdes conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Field Study Permissions

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

The required research permits to conduct fieldwork in Indonesia were provided by the Indonesian Ministry of Research, Technology, and Higher Education (RISTEKDIKTI).

Data Deposition

The following information was supplied regarding data availability:

DNA-Sequence information is accessible at the European Nucleotide Archive (ENA) under accession number PRJEB18570.

Funding

The authors received no funding for this work.


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