Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems

Abstract

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

Figure 1

Taxonomic structure and diversity of the reads mapping to Bacteria. Kingdom, phyla and class divisions across the four sampling locations in Kerala, India, with class divisions noted across the top four phyla.

Figure 2

Taxonomic structure and diversity of the reads mapping to Archaea. Kingdom, phyla and class divisions across the four sampling locations in Kerala, India, with class divisions noted across the top three phyla.

Figure 3

Taxonomic structure and diversity of the reads mapping to Eukaryota. Kingdom, phyla and class divisions across the four sampling locations in Kerala, India, with class divisions noted across the top four phyla.

Figure 4

Geographic locations and diversity in the sampling sites in the mangrove ecosystem of Kerala, India. Genera with more than 1% of the mapped reads are listed, with their rank and indications of their abundance are shown, and organisms shared across sampling locations are indicated by shading or boxes. (Image source: http://www.d-maps.com/carte.php?num_car=24853&lang=en andInkscapev0.92 was used for sample site labelling).

Figure 5

Principal Component Analysis and geographic location of samples compared across the globe. A. PCA analysis comparing mangrove forests, a rain forest, and four ocean sediment samples. B. Geographic locations of the samples that were compared in this analysis. (Image source- Link:https://commons.wikimedia.org/wiki/File:BlankMap-World-noborders.pngand Inkscape v0.92 was used for labelling).

Figure 6

Taxonomic structure at the highest taxonomic levels across all samples. Averages of reads across samples from the same geographic location are pictured, with diversity at the kingdom level (large circles), different phyla within those kingdoms (smaller circles), and classes presented.

Figure 7

Subsystem functional analysis of representatives from each of the ecosystems analyzed showing the top ten subsystems that the reads were assigned to. Reads that map to genes assigned to specific subsystems are demonstrated for a single representative from each geographic location compared.