Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Abstract

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Keywords: Yucatan Peninsula; coastal prokaryotic communities; metagenomic.

Figure 1

Relative abundance of bacteria composition across the four wetland sampling sites at phylum (upper) and family (bottom) levels. Conserved sites: Bocas de Dzilam and El Palmar; contaminated sites: Progreso and Sisal. X-axis: sampled locations (including the year). Y-axis: relative abundance of taxon.

Figure 2

Alpha diversity measures of the microbial communities of conserved sites (Bocas de Dzilam and El Palmar) and contaminated sites (Progreso and Sisal). Left: Observed diversity; Center: Chao 1 estimator diversity, the bar shows the standard error of the estimator; Right: Shannon index diversity. X-axis: Analyzed environments. Y-axis: Alpha diversity measure.

Figure 3

DPCoA of contaminated (Progreso and Sisal) and conserved (Dzilam and El Palmar) locations. Scatterplot of the first two principal axes of the DPCoA. Each geometric figure represents an individual sample, square: Bocas de Dzilam; circle: El Palmar; triangle: Progreso; diamond: Sisal. Each color represents an environmental state; green: conserved; orange: contaminated.

Figure 4

Microbial landscape of the Yucatan coast. Changes in the diversity and abundance of microbial species present in four locations on the Yucatan coast are observed.

Figure 5

Metataxonomic profile comparisons of differentially phylotypes between conserved sites (Bocas de Dzilam and El Palmar) and contaminated sites (Progreso and Sisal) using Statistical Analysis of Metagenomic Profiles (STAMP) analysis. (A): Phylum level. (B): Family level. A positive difference between proportions denotes a greater abundance in conserved group (blue bar), whereas a negative difference between proportions shows a greater abundance in contaminated group (orange bar) for the given phyla or family; the standard deviation is shown as a bar in the circles.

Figure 6

Metabolic pathways profile comparisons between conserved sites (Bocas de Dzilam and El Palmar) and contaminated sites (Progreso and Sisal) using STAMP analysis. Analyses were carried out at level 3 of specific pathway associated with a specific function using KEGG. Blue bar: conserved sites; orange bar: contaminated sites. The standard deviation is shown as a bar in the circles.

Figure 7

Metabolic pathways associated to biogeochemical (upper) and xenobiotics (bottom) functions.