Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Abstract

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.

Keywords: 16S rRNA gene amplicon sequencing; Mar Menor; coastal lagoon; microbial community; sediment.

FIGURE 1

Geographic location and sampling stations in the Mar Menor lagoon. Levels of different factors (depth, vegetation, and texture) are indicated by symbols (see legend at the right) for each sampling site. The symbols colored in gray indicate stations selected for microbiological studies.

FIGURE 2

Microbial cell concentrations for each Mar Menor sediment station and time of sampling in logarithmic scale. One replicate per station and sampling time is shown. Error bars indicate standard deviation in DAPI count.

FIGURE 3

(A) Number of OTUs (columns) and Shannon index estimates (dots) for rarefied samples. Deviation bars indicate variability within replicates of each station and sampling time. (B) Upset plot showing the OTU distribution (for OTUs > 0.1% relative abundance) along the 14 stations during the cold and warm seasons (March and September, respectively). At the top, columns indicate the number of OTUs shared by stations, which are marked at the bottom with black dots. Arrow indicates the core microbiome.

FIGURE 4

Distribution of bacterial and archaeal classes in Mar Menor sediments. Dot color and size indicate the relative abundance of each class. The main features of each station are shown at the bottom.

FIGURE 5

An NMDS plot of the Bray–Curtis distances among all samples (A), colored by factor texture (B), time (C), vegetation (D), depth (E), and zone (F).

FIGURE 6

Relative abundance of detected microbial classes based on the levels of factor texture (A), vegetation (B), depth (C), and zone (D). Error bars indicate the range of abundances within each group of samples. Mud (n = 66); Sand (n = 16); Cymodocea nodosa (n = 16); C. prolifera (n = 16); Shallow (n = 46); Intermediate (n = 24); Deep (n = 12); North (n = 18); Centre (n = 34); and South (n = 30). Asterisk (*) indicates statistically significant differences tested by ANOVA (p < 0.05).