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

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.The study of the microbial communities has been carried out within the project “Metafluidics” and it was funded by the European Union’s framework program Horizon 2020 (LEIT-BIO-2015-685474 to JA). Samplings were supported by the projects MEMM (financed by the Spanish Institute of Oceanography), 19-ESMARES2-ANG (financed by the Spanish Ministry of Ecological Transition and Demographic Challenge), and BIOFOM (Ref. TEC0004869 financed by the Regional Government of Murcia). M-DB and JB-E were supported by a contract within the Program Personal Técnico de Apoyo funded by the Ministerio de Economía y Competitividad. BA-R was also supported by the ACIF fellow of the Generalitat Valenciana government

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

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

Caracterización de las comunidades microbianas de los sedimentos del Mar Menor

La laguna costera del Mar Menor se sitúa en el sureste de España, concretamente en la región de Murcia. Se trata de una laguna somera, separada del Mar Mediterráneo por una estrecha franja de tierra denominada la Manga del Mar Menor. Debido a la singularidad del ecosistema y a los servicios ecosistémicos que genera, esta laguna se encuentra bajo diferentes figuras de protección medioambiental. Sin embargo, estas figuras no han impedido que la laguna se encuentre altamente afectada por presiones de origen antrópico como son los cambios hidrológicos, la eutrofización, la contaminación por residuos mineros así como por otro tipo de compuestos químicos. El Mar Menor y los efectos de estas presiones han sido estudiadas desde el punto de vista de las condiciones fisicoquímicas, la flora, la fauna o las redes tróficas. Sin embargo, solo existen dos trabajos sobre la microbiología del Mar Menor y la información que aportan es escasa y limitada a la columna de agua. No obstante, los sedimentos marinos presentan una elevada densidad microbiana así como una alta heterogeneidad metabólica por lo que tienen una gran influencia en los ciclos biogeoquímicos de estos ambientes. En la presente tesis se analizaron, por primera vez, las comunidades microbianas de los sedimentos del Mar Menor. En el Capítulo 1 se realizó una descripción de las comunidades microbianas de un total de 82 muestras de sedimentos, recogidas en dos puntos temporales, marzo y septiembre del año 2018, y por triplicado, de 14 estaciones de muestreo distribuidas por toda la laguna. Las comunidades microbianas se analizaron mediante la secuenciación de amplicones del gen del ARN ribosómico (ARNr) 16S y recuentos de DAPI en el contexto de varios factores y variables fisicoquímicas. Los resultados mostraron que existe una gran diversidad y heterogeneidad espacial. A nivel taxonómico, las clases principales fueron las Delta- y Gammaproteobacteria seguidos de Bacteroidia. Sin embargo, también se detectaron varios grupos taxonómicos poco conocidos hasta la fecha como son el filo Asgardarchaeota o las clases Woesearchaeia, WCHB1-81 o PAUC43f. Se identificaron a la textura (fango vs arena), la vegetación (Caulerpa vs Cymodocea), la profundidad (somera vs intermedia/profunda) y la zona (norte vs sur) como factores relevantes a la hora de estructurar las comunidades microbianas. Por otro lado, se observó que las estaciones de muestreo contaminadas con elementos potencialmente tóxicos o PTE (Pb, Zn, Cd y As) presentaban cambios temporales significativos mientras que las no contaminadas permanecían estables. Este comportamiento se investigó más en detalle y se concluyó que, probablemente, era debido a la presencia de una comunidad microbiana especializada para sobrevivir en ambientes con altas concentraciones de PTE pero con menor capacidad de adaptación antes cambios en otras variables ambientales en los sedimentos contaminados. Con respecto al Capítulo 2, con el objetivo de identificar las diferencias funcionales entre sedimentos colonizados por Caulerpa y Cymodocea, se realizó una comparación metagenómica y metatranscriptómica de estos sedimentos. Los resultados indicaron que los sedimentos colonizados por Caulerpa presentaban una comunidad microbiana más homogénea pero menos diversa funcionalmente que los sedimentos de Cymodocea. Además, las comunidades de los sedimentos de Caulerpa mostraron estar más especializadas en la degradación de materia orgánica con respecto a las de Cymodocea. El análisis de los genomas ensamblados a partir de los metagenomas (MAGs) reveló la presencia de microorganismos con una potencial capacidad pectinolítica. Finalmente, en este capítulo se identificó, gracias a los análisis metatranscriptómicos, una proteína que podría constituir una nueva CAZyme periplásmica no descrita hasta la fecha. En cuanto al Capítulo 3, se realizó un estudio ecológico, taxonómico y del potencial metabólico de PAUC43f, un grupo del filo Gemmatimonadota, detectado hasta el momento únicamente mediante secuencias del gen del ARNr 16S. PAUC43f se detectó en multitud de ecosistemas, principalmente en sedimentos marinos, esponjas y suelos salinos. Se identificaron 16 géneros dentro de este grupo, algunos de ellos claramente asociados a ambientes específicos. Además, se recuperaron los primeros 39 MAGs de PAUC43f que presentaron un potencial metabolismo quimioorganoheterótrofo y una respiración aerobia facultativa. Finalmente, se realizó una hibridación fluorescente in situ con sondas específicas para PAUC43f y se observó su morfología y estado metabólicamente activo en los sedimentos del Mar Menor. Esta tesis sirve como punto de partida para entender el papel de la microbiota de los sedimentos del Mar Menor en el funcionamiento del ecosistema.Tesis financiada por el proyecto de la Comisión Europea METAFLUIDICS GA 685474 y las ayudas para contratos predoctorales y estancias en el extranjero ACIF/2018 y BEFPI/2021 de la Generalitat Valenciana

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

The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment.This research was supported by the EU-H2020 MetaFluidics and Bluetools projects with grant agreement numbers 685474 and 101081957 (to J.A.). B.A.-R. is an ACIF fellow (Generalitat Valenciana)

Environmental dissolved DNA harbours meaningful biological information on microbial community structure

Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High‐speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.This research was supported by the Spanish Ministry of Science, Innovation and Universities grant MICROMATES (PGC2018-096956-B-C44), which was also supported with European Regional Development Fund (FEDER) funds, and by the Generalitat Valenciana grant PROMETEO/2017/129. B.A.-R. is a ACIF (Generalitat Valenciana) fellow

Spiribacter aquaticus sp. nov., a novel member of the genus Spiribacter isolated from a saltern

A moderately halophilic bacterium, designated strain SP30T, was isolated from a solar saltern located in Santa Pola, Alicante, on the East coast of Spain. It was a Gram-stain-negative, strictly aerobic bacterium, able to grow in 7.5–25 % (w/v) NaCl and optimally in 12.5 % (w/v) NaCl. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that the novel isolate is a member of the genus Spiribacter , with the most closely related species being Spiribacter roseus SSL50T (99.9 % sequence similarity) and Spiribacter curvatus UAH-SP71T (99.4 % sequence similarity). The 16S rRNA gene sequence similarity with the type species Spiribacter salinus M19-40T was 96.6 %. The DNA–DNA relatedness value between strain SP30T and S. roseus SSL50T and S. curvatus UAH-SP71T was 40 and 55 %, respectively; these values are lower than the 70 % threshold accepted for species delineation. The major fatty acids were C16:0, C18 : 1ω7c, C19 : 0 cyclo ω8c and C12 : 0. Similarly to other species of the genus Spiribacter , strain SP30Twas observed as curved rods and spiral cells. Metabolic versatility was reduced to the utilization of a few organic compounds as the sole carbon and energy sources, as with other members of Spiribacter. However, it differed in terms of colony pigmentation (brownish-yellow instead of pink) and in having a higher growth rate. Based on these data and on the phenotypic, genotypic and chemotaxonomic characterization, we propose the classification of strain SP30T as a novel species within the genus Spiribacter , with the name Spiribacter aquaticus sp. nov. The type strain is SP30T (=CECT 9238T=LMG 30005T).This work was supported by grants CGL2013-46941-P and CGL2015-66686-C3-3-P from the Spanish Ministerio de Economía y Competitividad, with European funds (FEDER)

Inverted microbial community stratification and spatial–temporal stability in hypersaline anaerobic sediments from the S’Avall solar salterns

The anaerobic hypersaline sediments of an ephemeral pond from the S’Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.This study was funded by the Spanish Ministry of Science, Innovation and Universities projects Salploma CLG2015_66686-C3-1-P, Micromates subprojects PGC2018-096956-B-C41 and PGC2018-096956-B-C44, and Marbiom RTC-2017-6405-1, which were also supported with European Regional Development Fund (FEDER) funds. RRM acknowledges the financial support of a sabbatical stay at Georgia Tech through the grant PRX18/00048 and also FFV’s for the support of her PhD with the fellowship BES-2016-078138, both from the Spanish Ministry of Science, Innovation and Universities