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.

Distribution, abundance, and ecogenomics of the Palauibacterales , a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

“…Furthermore, the Palauibacterales might have another restoring effect on the environment. In a recent study of Mar Menor (Spain) marine sediments, we observed a high relative abundance of PAUC43f in heavy-metal contaminated sediments ( 36 ). The most abundant PAUC43f OTU in these sediments shared 99.3% identity to the 16S rRNA gene sequence found in Carthagonibacter metallireducens (Sp.…”

“…A dataset was built with complete and partial 16S rRNA gene sequences, classified as “ PAUC43f marine benthic group ” retrieved from SILVA r138 database ( 34 ), marine invertebrates (corals and sponges from the Mediterranean Sea ( 35 )), and sediments from the Mar Menor lagoon (SE, Spain ( 36 )). For the following bioinformatic analyses, default settings were used unless otherwise noted.…”

“…MAGs belonging to Gemmatimonadota were searched in the GTDB release 207 ( 48 ) and GEM databases ( 49 ) as well as in other public sources ( https://data.ace.uq.edu.au/public/sponge_mags/ ; ( 22 , 23 , 50 )) and Mar Menor sediments samples described in ( 36 ). DNA from Mar Menor sediments (stations 2, 3, 5, 10, 13, 20, and 21) was extracted with the DNeasy PowerSoil kit (Qiagen) following the manufacturer’s indications, and metagenomes were sequenced on an Illumina Novaseq 6000 2×150 bp run in the CNAG (Barcelona, Spain).…”

“…To get experimental information (presence, activity, morphology, and size) about PAUC43f, PCR primers and FISH probes were designed using DECIPHER ( 74 ) and PrimerQuest Design Tool (IDT, https://eu.idtdna.com/PrimerQuest/Home/Index ). Since Mar Menor sediment samples (Murcia, Spain; 37°45'N 0°47'W), where PAUC43f had been previously detected, were readily accessible to our lab, we designed primers and probes against the 16S rRNA gene sequences of PAUC43f retrieved from these sediments ( 36 ). In silico quality control was performed using the OligoAnalyzer Tool (IDT, https://eu.idtdna.com/pages/tools/oligoanalyzer ), searching for secondary structures and dimerization, while probe specificity was checked with TestProbe against the SILVA database ( 34 ).…”

Exploring the sediment-associated microbiota of the Mar Menor coastal lagoon

“…Many of these negative impacts could also affect the sediment-associated microbiota, which is not only an important contributor to biogeochemical cycles but could also help to counteract these impacts by accumulating and managing nutrients and contaminants (Dash et al, 2013;Nzila, 2013;Rodrıǵuez et al, 2018). However, our knowledge of the microbial communities in the Mar Menor remains quite limited (Aldeguer-Riquelme et al, 2022).…”