Metagenomes of Mediterranean coastal lagoons

Abstract

Coastal lagoons, both hypersaline and freshwater, are common, but still understudied ecosystems. We describe, for the first time, using high throughput sequencing, the extant microbiota of two large and representative Mediterranean coastal lagoons, the hypersaline Mar Menor, and the freshwater Albufera de Valencia, both located on the south eastern coast of Spain. We show there are considerable differences in the microbiota of both lagoons, in comparison to other marine and freshwater habitats. Importantly, a novel uncultured sulfur oxidizing Alphaproteobacteria was found to dominate bacterioplankton in the hypersaline Mar Menor. Also, in the latter prokaryotic cyanobacteria were almost exclusively comprised by Synechococcus and no Prochlorococcus was found. Remarkably, the microbial community in the freshwaters of the hypertrophic Albufera was completely in contrast to known freshwater systems, in that there was a near absence of well known and cosmopolitan groups of ultramicrobacteria namely Low GC Actinobacteria and the LD12 lineage of Alphaproteobacteria.

Figure 1. Pairs of microphotographs, DAPI stain (blue, up) and photosynthetic pigment autofluorescence (red, down) of samples from Albufera (A and B) and Mar Menor (C and D) showing different microorganisms.

A) a colony of unicellular picocyanobacteria B) several filamentous cyanobacteria and coenobia of the chlorophytes Pediastrum sp. and Scenedesmus sp. C) Different morphologies of heterotrophic bacterioplankton (cells not showing red autofluorescence in lower pictures) and autotrophic picocyanobacteria (cells showing red autofluorescence in lower pictures). D) Heterotrophic bacterioplankton and autotrophic picocyanobacteria with a eukaryotic nanoflagellate. White bar corresponds to 10 μm in all pictures.

Figure 2. Cross comparison of comparative distribution 16S rRNA sequences from selected abundant high level bacterial taxa from Mar Menor and Albufera metagenomes to several freshwater and saline metagenomes.

Results from all filters have been combined.

Figure 3. Fragment recruitment plots of selected organisms versus the Mar Menor and the Albufera metagenomes.

The comparisons were done using BLASTN, and a minimum length of 50 bp and an evalue of 1e-5 was considered a hit. The X-axis is scaled in Mb and the Y-axis shows the %identity.

Figure 4. PCA of tetranucleotide frequencies of assembled contigs from Mar Menor and Albufera.

Only those contigs longer than 2 kb that had a consistent phylogenetic profile are shown (see methods).

Figure 5. Classification of actinobacterial 16S Reads from Albufera, Mar Menor and several other metagenomic datasets into known lineages of freshwater Actinobacteria.

The numbers above the bars indicate the total number of actinobacterial 16S sequences detected in each dataset.

Figure 6. PCA of tetranucleotide frequencies of actinobacterial contigs from Mar Menor.

For reference, actinobacterial contigs from Lake Gatun, Punta Cormoran and three fosmids from Lake Kinneret fosmids are also included. Six clusters of contigs are indicated, and the total sequence,mean contig length, and GC% range, and likely phylogenetic affiliation of the cluster are also shown.