Beyond the Iron Age: The ecological relevance of bioactive trace metals other than Fe and organic growth factors in aquatic systems

In the last three decades, research has extensively focused on the role of Fe and other mineral nutrients in regulating biological processes, ranging from the surface to the deep ocean. This has produced major breakthroughs in our understanding of the fundamental role of those bioactive elements on the carbon, nitrogen and sulfur cycles and ecosystem function. However, biological processes cannot be entirely sustained by that small set of chemical elements, and new scientific evidence suggests that trace metals other than Fe (e.g., Co, Mo and Ni) as well as essential organic growth factors (e.g., vitamins) may also be crucial in most aquatic systems

Partitioning of prokaryotic community structure and prokaryotic function by basin, depth and water mass across the Mediterranean Sea and the adjacent Atlantic Ocean

1st Iberian Ecological Society Meeting (2019); XIV Congreso Nacional de la Asociación Española de Ecología Terrestre (AEET), Ecology: an integrative science in the Anthropocene, 4-7 February 2019, Barcelona, SpainThe Mediterranean Sea is a unique small-scale ocean with a few remarkable characteristics: the deep waters are warm (minimal temperature is ca. 12°C), has strong east-to-west gradients in nutrient availability and phosphorous limitation and in relative water transparency, and various shallow sills partition it into clearly defined basins, with the coexistence of different varieties of deep water masses in the bathypelagic. These characteristics strongly contrast with those of the nearby North Atlantic Ocean at the same latitude. Understanding the characteristics of the Mediterranean prokaryotes might illustrate what to expect in a future more oligotrophic global ocean. In May 2014 we sampled an E to W transect in the Mediterranean that also included a few stations in the North Eastern Atlantic Ocean. We compared the structure of the prokaryotic communities in all these basins using flow cytometry and high-throughput sequencing of the 16S rDNA gene, and the potential activity using radioactive tracers (tritiated leucine) and metagenomics. In the deep waters we defined water masses and studied their characteristic microbial and genetic imprints. We will discuss the characteristics of the microbes thriving in the Mediterranean ocean by basin, depth layer and water mass, alongside with a discussion of the factors that determine the changes in the activity, abundance, single-cell properties, community structure and genomic potential across these habitatsPeer Reviewe

Active bacteria and archaea cells fixing bicarbonate in the dark along the water column of a stratified eutrophic lagoon

15 páginas, 4 tablas, 3 figuras.We studied the carbon dioxide fixation activity in a stratified hypereutrophic karstic lagoon using a combination of fingerprinting techniques targeting bacterial and archaeal 16S rRNA genes, functional gene cloning [the acetyl-CoA carboxylase (accC)], and isotopic labelling (14C-bicarbonate) coupled to single-cell analyses [microautoradiography combined with catalyzed reported deposition-FISH (MAR-CARD-FISH)]. The microbial planktonic community was dominated by bacteria with maximal abundances of archaea just below the oxic/anoxic transition zone (7% of total cells). In situ incubations with radiolabelled bicarbonate showed maximal photoassimilation activity in the oxic epilimnion, whereas dark CO2 fixation was consistently observed throughout the water column, with a maximum at the oxic/anoxic interface (8.6 mg C m−3 h−1). The contributions of light and dark carbon fixation activities in the whole water column were 69% and 31% of the total C incorporated, respectively. MAR-CARD-FISH incubations corroborated these results and revealed that the highest fraction of bacterial and archaeal cells actively uptaking bicarbonate in the light was found at the surface. The bacterial community was mainly composed of green sulfur bacteria (Chlorobi) and members of the Betaproteobacteria and the Bacteroidetes. The archaeal assemblage was composed of phylotypes of the Miscellaneous Crenarchaeotic Group and a few methanogens. Clone libraries of the accC gene showed an absolute dominance of bacterial carboxylases. Our results suggest that the dark carbon fixation activity measured was mainly related to CO2 incorporation by heterotrophs rather than to the activity of true chemoautotrophs.This study was funded through the projects VIARC (Ref. REN 2003-08333-GLO) and CRENYC (CGL2006-12058) to C.M.B. and E.O.C. from the Spanish Ministerio de Ciencia e Innovación (MCINN). M.L. and A.P. are recipients of PhD student fellowships from the Spanish government and the Generalitat de Catalunya, respectively.Peer reviewe

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

Riedel T, Gómez-Consarnau L, Tomasch J, et al. Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein. PLOS ONE. 2013;8(3): e57487.Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition