Identification and validation of microsatellite markers in strawberry tree (Arbutusunedo L.)

Strawberry tree (Arbutus unedo L.), an evergreen shrub/small tree of the family Ericaceae, is a main constituent of the Mediterranean basin flora; although it is also found in southwestern Prance, Macaronesia, and Ireland. The small fruits are edible but mostly used for preparation of preserves and jams, and for liquors such as the Portuguese traditional "aguardente de medronho". Traditionally cultivated by small farmers, often in consociation with Quercus sp., strawberry tree is presently emerging as a new important fruit crop cultivated in large orchards by modern export-oriented enterprises. This change of paradigm requires a growing role of plant breeding, upstream of the production process. Genomic tools for this species are mostly limited to the chloroplast genome sequence and to genomic data described in this work. In order to identify strawberry tree microsatellite (SSR) loci we performed partial genome next-generation sequencing using the Ion Torrent technology. The sequenced similar to 24.6M nucleotides resulted in the identification of 1185 microsatellite markers mostly constituted by dinucleotide motifs. The relative amount of microsatellite dinucleotide motifs (AG/CT - 71.7%, AC/GT - 20.5%, AT/AT - 2.9%, and CG/CG - 0.3%) is similar to the one observed in other Ericaceae species. Among a tested sample of 40 SSR primer pairs, 20 amplified well-defined PCR products, 12 (30%) were validated as polymorphic. Used in our collaborative project for molecular identification of selected and improved clones, the identified SSR loci constitute a strong tool for a large panoply of applied and fundamental studies of this emerging fruit crop.Pluriannual Funding Program of the Portuguese National Foundation for Science and Technologyinfo:eu-repo/semantics/publishedVersio

Recovery of catalytic metals from leaching solutions of spent automotive catalytic converters using plant extracts

This study investigates the potential of hydroalcoholic extracts of Cistus ladanifer L., Erica Andevalensis and Rubus idaeus L. as a green method for the recovery of platinum group metals (PGMs) from both synthetic unimetallic solutions and multimetallic solutions obtained from the leaching of two different spent automotive catalytic converters (SACC). Experiments with unimetallic solutions revealed that E. andevalensis and R. idaeus extracts could separate about 70% of Pd and less than 40% of other tested metals (Al, Ce, Fe and Pt) from the solutions. Then, application of the plant extracts to two different SACCs leachates showed that E. andevalensis and R. idaeus extracts can induce high precipitation (> 60%) of Pd and Pt with co-precipitation of less than 20% of other metals. UV-Visible spectra analysis confirmed the bio-reduction of Pd2+ ions into Pd-0 nanoparticles by R. idaeus extract, and Fourier transform infrared spectroscopy (FTIR) analysis revealed the contribution of functional groups of the phytochemicals present in the extract (such as phenols, flavonoids and anthocyanins) in the Pd2+ bio-reduction and stabilization. Afterward, scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) analysis of the precipitate obtained from one leachate with R. idaeus extract demonstrated the presence of Pd particles along with organic compounds and particles containing other metals. Therefore, particles were subjected to a washing step with acetone for further purification. Finally, scanning transmission electron microscopy with energy dispersive X-ray spectroscopy (STEM-EDX) analysis showed the high purity of the final Pd particles and high-resolution STEM allowed to determine their size variation of 2.5 to 17 nm with an average Feret size of 6.1 nm and confirmed their crystalline structure with an interplanar lattice distance of similar to 0.22 nm. This green approach offers various benefits including simplicity of Pd separation from the leachates as valuable nanoparticles that makes the process more feasible from economic and environmental standpoints. A process cost of similar to 20 $/g of Pd particles recovered was estimated (excluding manpower).LA/P/0101/2020; CRESC Algarve 2020) through Portugal 2020 and European Regional Development Fund (FEDER), under the project METALCHEMBIO (no. 29251).info:eu-repo/semantics/publishedVersio

Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria

The 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level.info:eu-repo/semantics/publishedVersio

Growth, photosynthetic pigments, phenolic content and biological activities of Foeniculum vulgare Mill., Anethum graveolens L. and Pimpinella anisum L. (Apiaceae) in response to zinc

The effect of zinc (Zn) on phenols, antioxidant activities (free radicals' scavenging activities, inhibition of lipid peroxidation, chelating activity and reducing power), and enzyme inhibition activities of acetylcholinesterase, lipoxygenase and tyrosinase of anise, dill and two cultivars of fennel [Latina" (F-L) and "Doux de Florence" (F-DF)] aqueous extracts was evaluated for the first time. At the same time, growth and photosynthetic pigment contents were also estimated. A significant decrease in all growth parameters, such as plant height, fresh and dry weights of aerial parts and roots was statistically proved in the presence of 2 mM Zn. An enhancement of Zn accumulation was observed, particularly in aerial part. Exposure to 2 mM Zn induced quantitative changes in the phenols of all tested extracts. In fennel extracts, a decrease of phenol content was observed when treated with Zn, whereas an increase was found in dill and anise extracts submitted to Zn treatment. All samples, either in the presence or absence of Zn, showed antioxidant activity, independent on the tested assay, with the exception of the cultivar F-DF (treated and non-treated), which was unable to scavenge NO radicals. Zn-treated dill and anise presented usually higher antioxidant activity. Concerning inhibitory activities against acetylcholinesterase, lipoxygenase and tyrosinase enzymes, both treated and non-treated F-DF did not inhibit acetylcholinesterase activity. Zinc-treated F-DF was also unable to inhibit lipoxygenase activity. The remaining species presented capacity for inhibiting those enzymes and tyrosinase as well, but their abilities varied in response to Zn excess.Portuguese National Funding Agency for Science, Research and Technology (Fundacao para a Ciencia e a Tecnologia - FCTPortugal) [UID/BIA/04325/2013-MEDTBIO, UID/Multi/04326/2013]info:eu-repo/semantics/publishedVersio

Mapeamento genético do ananaseiro (Ananas comosus (L.) Merrilll)

Tese dout., Biologia, Universidade do Algarve, 2006The main aim of this thesis was the construction of a Pineapple (Ananas comosus (L.) Merrill) genetic reference map. Based on an (A. comosus var. comosus X Ananas comosus var. bracteatus) F1 population, two genetic maps, one for each progenitor, were assembled. Subsequently, a new map integrating markers from both progenitors was constructed on the basis of an F2 population. Using markers segregating simultaneously among the F1 and F2 populations, an integrated map was constructed gathering 783 molecular markers (588 AFLP, 137 RAPD, 57 ISSR, and the PGM isozyme locus) and the morphological trait locus “piping” into 77 linkage groups. In view of the facts that (1) in the integrated map, 31 linkage groups (a number close to the 25 pineapple chromosomes) are longer than 50cM; (2) that the different maps span over 60.7% to 91.4% of the genome, and; (3) that marker density is moderately high, with 4.16 cM average distance between markers, it is legitimate to suppose that these first genetic maps of pineapple will be very useful for construction of physical maps, for genome sequencing and for gene isolation via map-based cloning in this crop species.Fundação para a Ciência e a Tecnologia (FCT

Potential of industrial by-products and wastes from the Iberian Peninsula as carbon sources for sulphate-reducing bacteria

Industrial by-products and wastes from Portugal and Spain were tested for the first time as carbon sources/electron donors for sulphate-reducing bacteria. Cultures in mineral medium supplemented with the tested substrates were monitored, and sulphate reduction efficiency is discussed in light of substrates compositions, dosages and corresponding chemical oxygen demand/[SO42-] ratios. The results reveal the ability of those substrates to feed SRB and confirm that testing doses targeting ratios of 1.5 and values close to this was a good strategy to optimize sulphate reduction activity. As expected, this activity was faster for substrates that have in their composition simple compounds (such as low-chain alcohols and organic acids) and/or compounds that can be rapidly degraded (such as sugars), though it also occurred in a longer-term perspective with substrates composed mainly of slowly degradable compounds (such as cellulose and lignin). Thus, this work demonstrates the potential of new substrates and respective required doses to feed SRB bioreactors in long-term passive bioremediation processes or faster more active processes. That is, it opens the way for the use of such substrates in the treatment of sulphate-rich waters, as the acid mine drainage generated in some mines on the Iberian Pyrite Belt region, and it encourages further experiments to evaluate the use of SRB-based processes to treat the industrial wastewaters successfully tested in this work themselves, specially the olive mill wastewater which is still a problem for many small olive oil producers.European UnionEuropean Union (EU) [619101]Portuguese Foundation for Science and Technology (FCT)Portuguese Foundation for Science and Technology [UID/Multi/04326/2019]info:eu-repo/semantics/publishedVersio

Feasibility of co-treating olive mill wastewater and acid mine drainage

Previous tests using a growth medium and olive mill wastewater (OMWW) have shown that it supplies carbon and electron donors suitable for sulphate reducing bacteria (SRB). We assessed the co-treatment of acid mine drainage (AMD) and OMWW using SRB-enriched bioreactors and identified the most abundant bacterial populations present under optimized conditions. The process requires a neutralizing agent to create optimal pH conditions for successful removal of the AMD's main contaminants. Concentrations of SO42-, Al, Fe, Cu, Zn, and Mn decreased to below Portugal's maximum admissible values for irrigation waters, and all but Mn were reduced to less than Portugal's emission limit values (ELVs) for wastewater discharges. Phenol concentrations-the main pollutants in OMWW-dropped to values between 1/10 and 1/5 their initial concentrations in batch tests using mixtures of AMD and OMWW, and to 1/2 their initial concentrations in flow-through tests. The final total phenol concentrations were still above the ELV for wastewater discharges, but phenols are not regulated in irrigation waters, and OMWW is used by some producers to irrigate soils. Six main SRB groups were identified as likely having a fundamental role in the bioremediation process: the generaDesulfovibrio,Sulfurospirillum, andAcetobacterand the familiesSphingomonadaceae,Prevotellaceae, andDeferribacteraceaeFCT: UIDB/04326/2020; European Union (EU): 619101; FCT - Algarves Regional Operational Program (CRESC Algarve 2020) through Portugal 2020: 29251info:eu-repo/semantics/publishedVersio

Potential use of agricultural waste—Carob Kibbles (Ceratonia siliqua L.) as a biosorbent for removing boron from wastewater

The release of boron (B) into the environment as a result of anthropogenic activity modifies sustainable natural conditions, thus affecting ecosystems. To meet water quality regulations, commercial and natural boron adsorbents are available to reduce its concentrations in industrial effluents, with the former being not only more expensive but also less sustainable. In the publication, the biosorption parameters of carob kibbles (Ceratonia siliqua L.) were optimized in order to remove boron from aqueous solutions using batch experiments. The biosorbent used in the present research was agro-waste biomass provided by the local locust-beam gum industry. Boron removal by carob kibbles was favored at high initial pH values, and this capacity was found to be a function of boron initial concentration, biosorbent content in the solution, and particle size. The change in temperature did not affect the potential of biomass to remove boron. The highest boron removal efficiency (55.1%) was achieved under the following optimal conditions: 50 g/L biosorbent dose (Cs), with particle size range 0.025–0.106 mm, for the initial concentration (C0) of boron in the solution of 100 mg/L, at an initial pH of 11.5, for 5 h at 25 °C. This investigation suggests that carob kibble agro-waste can be valorized as a biosorbent to remove boron from wastewater, and the boron-loaded residue may eventually be explored as a new boron-fertilizer.METALCHEMBIO project (no. 29251); CRESC Algarve 2020; LA/P/0101/2020.info:eu-repo/semantics/publishedVersio

Multi-element characterisation of carob, fig and almond liqueurs by MP-AES

Carob pod, fig and almond liqueurs are produced in various Mediterranean regions. This work reports the mineral content of these traditional beverages and evaluates the influence of the raw material. Twenty-five fruit liqueurs from 16 producers were analysed. A simple open-vessel sample mineralization by wet digestion using nitric acid-hydrogen peroxide (1:1) was used before spectrometric analysis. Nine essential elements (Cu, Ca, Mg, Na, K, Fe, Zn, Mn and P) and two non-essentials (Cd and Pb) were quantified by microwave plasma-atomic emission spectrometry (MP-AES). Carob liqueur presented the broader profile of minerals and was the only fruit liqueur containing iron (72.7% of samples), phosphorous, manganese and low levels of lead (in two of the 11 samples). Conversely, almond liqueurs contained the lowest mineral content with only five elements detected. Fruit liqueurs showed variability in mineral content even within the same liqueur, presumably as a consequence of the different manufacturing processes. Despite this variability, application of principal component analysis to essential mineral concentrations (K, Na, Ca, Mg, Mn, Fe and Zn) resulted in satisfactory classification (PC1 and PC2 accounting for 78.5% of the total variance) of the Portuguese liqueurs evaluated.SFRH/BPD/103086/2014info:eu-repo/semantics/publishedVersio

Putative role of flavobacterium, dokdonella and methylophilus strains in paracetamol biodegradation

Paracetamol, the most widely and globally used analgesic and antipyretic, is easily accumulated in aquatic environments. In the present study, the biodegradation of paracetamol in different media (one for general growth, one specific for sulfate reducing bacteria, a mineral salts medium and municipal wastewater) inoculated with two types of sludge (from anaerobic lagoon and from oxidation ditch) under different oxygenic conditions (anoxic; moderate oxygenation in open flasks and high oxygenation by aeration) was investigated. In addition, bacteria with relative abundances increasing simultaneously with paracetamol degradation, when this drug was the only carbon source, thus with a putative role in its degradation, were identified using 16S rRNA gene sequences. The results show that aerobic microorganisms had a major role in the degradation of paracetamol, with 50 mg/L totally removed from municipal wastewater after 2 days incubation with aeration, and that the metabolites 4-aminophenol and hydroquinone plus one compound not identified in this work were produced in the process. The identification of bacteria with a role in the degradation of paracetamol revealed a strain from genus Pseudomonas with the highest final relative abundance of 21.2%, confirming previous works reporting strains of this genus as paracetamol decomposers. Besides, genera Flavobacterium, Dokdonella and Methylophilus were also in evidence, with initial relative abundances of 1.66%, 1.48 and 0.00% (not detected) in the inoculum and 6.91%, 3.80 and 3.83% after incubation, respectively. Therefore, a putative role of these genera in paracetamol biodegradation is suggested for the first time.Erasmus Mundus Master in Chemical Innovation and Regulations (EMMC-ChIR) of Donaldben Mbagag NEBA by the Erasmus Mundus program of the European Commissioninfo:eu-repo/semantics/publishedVersio