Testing of the CHEMTAX program in contrasting Neotropical lakes, lagoons, and swamps

ABSTRACT: The problem using the CHEMTAX program in freshwater environments is that the few matrices of pigment ratios available have not been tested in a wide range of environments. Sixteen Amazonian, Andean, and Caribbean lakes, lagoons, and swamps were sampled over a year. The aim was to determine if it was possible to obtain a reliable matrix of input pigment ratios that may be used in freshwater habitats with different environmental conditions. There were no clear differences among regions for most of the ratios of marker pigments to Chlorophyll a (Chl a) in most of the phytoplankton groups. Only the zeaxanthin/Chl a ratio showed clear variations among areas. The estimates for the mean relative contribution of each phytoplankton group calculated for the pigment ratios obtained in each separate habitat and season were very similar to the estimates calculated using the average pigment ratio obtained for all habitats and seasons. Our study suggests that the matrix of the average pigment ratio obtained in this study can be used to estimate phytoplankton class abundances with the CHEMTAX program in freshwater habitats with different limnological conditions

Data series

This excel file contains all the raw data from the manuscript. Each sheet is named with the figure number to which its data belong. The column headings indicate the figure panel to which the data belong, and below, the variables

Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species

Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC-MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).Funding Agencies|European Union (Interreg POCTEP, project ACUINANO) [07-12-ACUINANO_1_E]; Portuguese Foundation for Science and Technology (Fundacao para a Ciencia e Tecnologia; FCT)Portuguese Foundation for Science and Technology [UIDB/04423/2020, UIDP/04423/2020]; European Regional Development Fund (ERDF)European Commission</p

Structure-Antifouling Activity Relationship and Molecular Targets of Bio-Inspired(thio)xanthones

The development of alternative ecological and effective antifouling technologies is still challenging. Synthesis of nature-inspired compounds has been exploited, given the potential to assure commercial supplies of potential ecofriendly antifouling agents. In this direction, the antifouling activity of a series of nineteen synthetic small molecules, with chemical similarities with natural products, were exploited in this work. Six (4,5,7,10,15and17) of the tested xanthones showed in vivo activity toward the settlement ofMytilus galloprovincialislarvae (EC50: 3.53-28.60 mu M) and low toxicity to this macrofouling species (LC50&amp;gt; 500 mu M and LC50/EC50: 17.42-141.64), and two of them (7and10) showed no general marine ecotoxicity (Artemia salinamortality) after 48 h of exposure. Regarding the mechanism of action in mussel larvae, the best performance compounds4and5might be acting by the inhibition of acetylcholinesterase activity (in vitro and in silico studies), while7and10showed specific targets (proteomic studies) directly related with the mussel adhesive structure (byssal threads), given by the alterations in the expression ofMytiluscollagen proteins (PreCols) and proximal thread proteins (TMPs). A quantitative structure-activity relationship (QSAR) model was built with predictive capacity to enable speeding the design of new potential active compounds.Funding Agencies|FCT-Foundation for Science and TechnologyPortuguese Foundation for Science and Technology [UIDB/04423/2020, UIDP/04423/2020]; FCTPortuguese Foundation for Science and Technology [PTDC/AAG-TEC/0739/2014, POCI-01-0145-FEDER-016793]; ERDF-European Regional Development Fund through the COMPETE-Programa Operacional Factores de Competitividade (POFC) programme; RIDTI-Reforcar a Investigacao, o Desenvolvimento Tecnologico e a Inovacao [9471]; project NASCEM - FCT, COMPETE2020 [PTDC/BTA-BTA/31422/2017, POCI-01-0145-FEDER-031422]; PORTUGAL2020</p

Bioprospecting for industrially relevant exopolysaccharide-producing cyanobacteria under Portuguese simulated climate

Abstract Cyanobacterial exopolysaccharides (EPS) are potential candidates for the production of sustainable biopolymers. Although the bioactive and physicochemical properties of cyanobacterial-based EPS are attractive, their commercial exploitation is limited by the high production costs. Bioprospecting and characterizing novel EPS-producing strains for industrially relevant conditions is key to facilitate their implementation in various biotechnological applications and fields. In the present work, we selected twenty-five Portuguese cyanobacterial strains from a diverse taxonomic range (including some genera studied for the first time) to be grown in diel light and temperature, simulating the Portuguese climate conditions, and evaluated their growth performance and proximal composition of macronutrients. Synechocystis and Cyanobium genera, from marine and freshwater origin, were highlighted as fast-growing (0.1–0.2 g L−1 day−1) with distinct biomass composition. Synechocystis sp. LEGE 07367 and Chroococcales cyanobacterium LEGE 19970, showed a production of 0.3 and 0.4 g L−1 of released polysaccharides (RPS). These were found to be glucan-based polymers with high molecular weight and a low number of monosaccharides than usually reported for cyanobacterial EPS. In addition, the absence of known cyanotoxins in these two RPS producers was also confirmed. This work provides the initial steps for the development of cyanobacterial EPS bioprocesses under the Portuguese climate

Proteomics reveals multiple effects of titanium dioxide and silver nanoparticles in the metabolism of turbot, Scophthalmus maximus

Titanium dioxide (TiO2) and silver (Ag) NPs are among the most used engineered inorganic nanoparticles (NPs); however, their potential effects to marine demersal fish species, are not fully understood. Therefore, this study aimed to assess the proteomic alterations induced by sub-lethal concentrations citrate-coated 25 nm ("P25") TiO2 or polyvinylpyrrolidone (PVP) coated 15 nm Ag NPs to turbot, Scophthalmus maximus. Juvenile fish were exposed to the NPs through daily feeding for 14 days. The tested concentrations were 0, 0.75 or 1.5 mg of each NPs per kg of fish per day. The determination of NPs, Titanium and Ag levels (sp-ICP-MS/ICP-MS) and histological alterations (Transmission Electron Microscopy) supported proteomic analysis performed in the liver and kidney. Proteomic sample preparation procedure (SP3) was followed by LC-MS/MS. Label-free MS quantification methods were employed to assess differences in protein expression. Functional analysis was performed using STRING web-tool. KEGG Gene Ontology suggested terms were discussed and potential biomarkers of exposure were proposed. Overall, data shows that liver accumulated more elements than kidney, presented more histological alterations (lipid droplets counts and size) and proteomic alterations. The Differentially Expressed Proteins (DEPs) were higher in Ag NPs trial. The functional analysis revealed that both NPs caused enrichment of proteins related to generic processes (metabolic pathways). Ag NPs also affected protein synthesis and nucleic acid transcription, among other processes. Proteins related to thyroid hormone transport (Serpina7) and calcium ion binding (FAT2) were suggested as biomarkers of TiO2 NPs in liver. For Ag NPs, in kidney (and at a lower degree in liver) proteins related with metabolic activity, metabolism of exogenous substances and oxidative stress (e.g.: NADH dehydrogenase and Cytochrome P450) were suggested as potential biomarkers. Data suggests adverse effects in turbot after medium/long-term exposures and the need for additional studies to validate specific biological applications of these NPs.Funding: European Regional Development Fund (ERDF) through Interreg Atlantic Area Program, project NANO -CULTURE [EAPA 590/2018]; Portuguese Foundation for Science and Technology (Fundacao para a Ciencia e Tecnologia; FCT) [UIDB/04423/2020, UIDP/04423/2020]</p