Small tropical islands with dense human population: Differences in water quality of near-shore waters are associated with distinct bacterial communities
- Published
- Accepted
- Subject Areas
- Biodiversity, Marine Biology, Microbiology, Environmental Impacts
- Keywords
- Spermonde Archipelago, eutrophication, small islands, bacterial community composition, TEP
- Copyright
- © 2018 Kegler et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Small tropical islands with dense human population: Differences in water quality of near-shore waters are associated with distinct bacterial communities. PeerJ Preprints 6:e26553v1 https://doi.org/10.7287/peerj.preprints.26553v1
Abstract
Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles and back reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands are associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon (DOC) and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Raw R-code for the submitted analyses
This is the provided raw code for the conducted bioinformatics analyses in R.
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.
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.
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.
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.
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.
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.
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.
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).
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.