Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum
- Published
- Accepted
- Subject Areas
- Bioinformatics, Ecosystem Science, Genomics, Marine Biology, Natural Resource Management
- Keywords
- 16S rRNA sequencing, metabarcoding, descriptive analysis
- Copyright
- © 2018 Kaimenyi 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. Microbiome of two predominant seagrass species of the Kenyan coast, Enhalus acoroides and Thalassodendron ciliatum. PeerJ Preprints 6:e27387v1 https://doi.org/10.7287/peerj.preprints.27387v1
Abstract
Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs and mangrove forests with little direct action taken to conserve seagrass meadows. Pollution, over-exploitation of marine resources and minimal efforts towards enforcement of conservation laws of marine environments, have caused degradation and defoliation of seagrass habitats. Little is known about the microbes associated with seagrass species in Kenya and this study aimed to characterize the genetic diversity of the microbiomes of two prominent seagrass species, Enhalus acoroides and Thallasodendron ciliatum, which are the most commonly occurring species.
Methods. Replicate microbiome samples were collected from leaves, roots, sediment and water columns associated with the two seagrass species from two sites on the Kenyan coast. The microbial communities of the samples were characterized and compared using 16S ribosomal RNA gene PCR and sequencing. Microbiome features including diversity and taxonomic composition were used to compare within and between sample types and sites.
Results. Leaf samples from both E. acoroides and T. ciliatum had significantly different microbial communities comparted to root and sediment samples, revealing a diversity gradient with lowest diversity in water samples and highest in sediment. There were no significant variation in seagrass microbial composition associated with leaf and rhizosphere microbiomes of either E. acoroides or T. ciliatum. However, we did see a difference between water samples associated with each seagrass species.
Discussion. This study of the microbiomes associated with the sediments, roots, leaves and surrounding water of E. acoroides and T. ciliatum, included a limited number of samples from a small geographic area, providing a valuable first assessment of the microbial diversity of seagrass beds on the Kenyan coast. We found no significant differences between the plant-associated bacterial communities of the two-seagrass species investigated. Significant differences however, were observed amongst leaf-, root-, sediment- and water-associated bacterial communities. This work will contribute to understanding the dynamic environment of seagrass beds and will contribute to helping conserving and re-establishing seagrass beds degraded by due to anthropogenic activities.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Supplementary table 1
Relative abundance at Phylum level
Supplementary table 2
Relative abundance at Class level