Metabolomic and Lipidomic Tools for Tracing Fish Escapes from Aquaculture Facilities.

During adverse atmospheric events, enormous damage can occur at marine aquaculture facilities, as was the case during Storm Gloria in the southeastern Spanish Mediterranean in January 2020, with massive fish escapes. Fishes that escape were caught by professional fishermen. The objective of this study was to identify biomarkers in fish that enable differentiation among wild fish, escaped farm-raised fish, and farm-raised fish kept in aquaculture facilities until their slaughter. We focused on gilthead sea bream (Sparus aurata). We used nuclear magnetic resonance to search for possible biomarkers. We found that wild gilthead sea bream showed higher levels of taurine and trimethylamine-N-oxide (TMAO) in their muscle and higher levels of ω-3 fatty acids, whereas farm-escaped and farmed gilthead sea bream raised until slaughter exhibit higher levels of ω-6 fatty acids. From choline, carnitine, creatinine, betaine, or lecithin, trimethylamine (TMA) is synthesized in the intestine by the action of bacterial microflora. In the liver, TMA is oxidized to TMAO and transported to muscle cells. The identified biomarkers will improve the traceability of gilthead sea bream by distinguishing wild specimens from those raised in aquaculture.

Beauveria bassiana (Hypocreales: Clavicipitaceae) Volatile Organic Compounds (VOCs) Repel Rhynchophorus ferrugineus (Coleoptera: Dryophthoridae).

The entomopathogenic fungus Beauveria bassiana (Bb) is used to control the red palm weevil (RPW) Rhyncophorus ferrugineus (Oliver). Beuveria bassiana can infect and kill all developmental stages of RPW. We found that a solid formulate of B. bassiana isolate 203 (Bb203; CBS 121097), obtained from naturally infected RPW adults, repels RPW females. Fungi, and entomopathogens in particular, can produce volatile organic compounds (VOCs). VOCs from Bb203 were analyzed using gas chromatography-mass spectrometry (GC-MS). GC-MS identified more than 15 VOCs in B. bassiana not present in uninoculated (control) formulate. Both ethenyl benzene and benzothiazole B. bassiana VOCs can repel RPW females. Our findings suggest that B. bassiana and its VOCs can be used for sustainable management of RPW. They could act complementarily to avoid RPW infestation in palms.

Thermogravimetry coupled with mass spectrometry successfully used to quantify polyethylene and polystyrene microplastics in organic amendments.

The global consumption of plastic is growing year by year, producing small plastic pieces known as microplastics (MPs) that adversely affect ecosystems. The use of organic amendments (compost and manure) polluted with MPs affects the quality of agricultural soils, and these MPs can be incorporated into the food chain and negatively impact human health. Current European legislation only considers large plastic particles in organic amendments. There is no information regarding MP pollution. Thus, the development of a methodology to support future legislation ensuring the quality of agricultural soils and food safety is necessary. This proposed methodology is based on thermogravimetry coupled with mass spectrometry to quantify polyethylene and polystyrene (PE and PS) MPs through their mass spectrometry signal intensity of characteristic PE (m/z 41, 43 and 56) and PS (m/z 78 and 104) ions. This method has been validated with several organic amendments where the MP content ranged from 52.6 to 4365.7 mg kg-1 for PE-MPs and from 1.1 to 64.3 mg kg-1 for PS-MPs. The proposed methodology is a quick and robust analytical method to quantify MPs in organic amendments that could support new legislation.

Estimation of parameters in sewage sludge by near-infrared reflectance spectroscopy (NIRS) using several regression tools.

Sewage sludge application to agricultural soils is a common practice in several countries in the European Union. Nevertheless, the application dose constitutes an essential aspect that must be taken into account in order to minimize environmental impacts. In this study, near infrared reflectance spectroscopy (NIRS) was used to estimate in sewage sludge samples several parameters related to agronomic and environmental issues, such as the contents in organic matter, nitrogen and other nutrients, metals and carbon fractions, among others. In our study (using 380 biosolid samples), two regression models were fitted: the common partial least square regression (PLSR) and the penalized signal regression (PSR). Using PLSR, NIRS became a feasible tool to estimate several parameters with good goodness of fit, such as total organic matter, total organic carbon, total nitrogen, water-soluble carbon, extractable organic carbon, fulvic acid-like carbon, electrical conductivity, Mg, Fe and Cr, among other parameters, in sewage sludge samples. For parameters such as C/N ratio, humic acid-like carbon, humification index, the percentage of humic acid-like carbon, the polymerization ratio, P, K, Cu, Pb, Zn, Ni and Hg, the performance of NIRS calibrations developed with PLSR was not sufficiently good. Nevertheless, the use of PSR provided successful calibrations for all parameters.

New approach for chemometric analysis of mass spectrometry data.

The search of metabolites which are present in biological samples and the comparison between different samples allow the construction of certain biochemical patterns. The mass spectrometry (MS) methodology applied to the analysis of biological samples makes it possible for the identification of many metabolites. Each obtained signal (m/z) is characteristic of a particular metabolite. However, the mass data (m/z) interpretation is difficult because of the large amount of information that they contain. In this work, we present a relatively simple tool that allows us to deal with the whole of the mass information from the chemometric analysis. The statistical analysis is a key stage in order to identify the metabolites involved in a particular biochemical pattern. We transformed the mass data matrix in a vector. By having the data as a vector, it was possible to keep all the information and also avoid the signals overlapping, which is the major problem when the total ion chromatogram (TIC) is obtained. In the approach proposed here, the mass data (m/z) matrix was split in 100 different TIC in order to avoid the signal overlapping. The 100 chromatograms were concatenated in a vector. This vector, which can be plotted as a continuous (2D pseudospectrum), greatly simplifies for one to understand the subsequent dimensional multivariate analysis. To validate the method, 19 samples from two human embryos culture medium were analyzed by high-pressure liquid chromatography-mass spectrometry (HPLC-MS). Our methodology would be applied to the obtained raw data. Later on, a multivariate analysis was conducted using a robust principal components analysis interval (robPCA) and interval partial least squares algorithm (iPLS). The results obtained allow one to differentiate the two sample populations undoubtedly, although their composition was similar.

Study of the evolution of organic matter during composting of winery and distillery residues by classical and chemometric analysis.

The aim of the present paper is to evaluate the changes of organic matter during the composting process of fresh winery and distillery residues (WDR) by means of classical and chemometric analysis of (13)C cross-polarization magic angle spinning (CPMAS) NMR and Fourier transform infrared (FT-IR) spectra. (13)C NMR spectroscopy displayed a preferential biodegradation of carbohydrates as well as an accumulation of aliphatic chains (cutin- and suberin-like substances). This preferential biodegradation of the organic fractions reduces the landfill emission potential. Although the composition of the input mixture strongly affects the shape of the infrared (IR) spectra, typical bands of components can be selected and used to follow the composting process; that is, changes in the relative absorbances of the band of nitrate (at 1384 cm(-1)) and in the band of carbohydrates (at 1037 cm(-1)) have been observed. In addition, different chemometric tools, such as partial least-squares (PLS), interval PLS (iPLS), backward iPLS (biPLS), and genetic algorithm (GA), have been used to find the most relevant spectral region during the composting process. Chemometric analysis based on the combined and sequential use of iPLS and GA has been revealed as a very powerful tool for the detection in samples of the most relevant spectral region related to the composting process. From the obtained results, it can be concluded that CPMAS (13)C NMR supported by FT-IR could provide information about the evolution and characteristics of the organic matter during the composting process in order to avoid contamination problems after its use as amendment in agriculture or after landfilling.

NO3-/NO2- assimilation in halophilic archaea: physiological analysis, nasA and nasD expressions.

The haloarchaeon Haloferax mediterranei is able to assimilate nitrate or nitrite using the assimilatory nitrate pathway. An assimilatory nitrate reductase (Nas) and an assimilatory nitrite reductase (NiR) catalyze the first and second reactions, respectively. The genes involved in this process are transcribed as two messengers, one polycistronic (nasABC; nasA encodes Nas) and one monocistronic (nasD; codes for NiR). Here we report the Hfx mediterranei growth as well as the Nas and NiR activities in presence of high nitrate, nitrite and salt concentrations, using different approaches such as physiological experiments and enzymatic activities assays. The nasA and nasD expression profiles are also analysed by real-time quantitative PCR. The results presented reveal that the assimilatory nitrate/nitrite pathway in Hfx mediterranei takes place even if the salt concentration is higher than those usually present in the environments where this microorganism inhabits. This haloarchaeon grows in presence of 2 M nitrate or 50 mM nitrite, which are the highest nitrate and nitrite concentrations described from a prokaryotic microorganism. Therefore, it could be attractive for bioremediation applications in sewage plants where high salt, nitrate and nitrite concentrations are detected in wastewaters and brines.

The effect of ammonium on assimilatory nitrate reduction in the haloarchaeon Haloferax mediterranei.

Physiology, regulation and biochemical aspects of the nitrogen assimilation are well known in Prokarya or Eukarya but they are poorly described in Archaea domain. The haloarchaeon Haloferax mediterranei can use different nitrogen inorganic sources (NO (3) (-) , NO (2) (-) or NH (4) (+) ) for growth. Different approaches were considered to study the effect of NH (4) (+) on nitrogen assimilation in Hfx. mediterranei cells grown in KNO(3) medium. The NH (4) (+) addition to KNO(3) medium caused a decrease of assimilatory nitrate (Nas) and nitrite reductases (NiR) activities. Similar effects were observed when nitrate-growing cells were transferred to NH (4) (+) media. Both activities increased when NH (4) (+) was removed from culture, showing that the negative effect of NH (4) (+) on this pathway is reversible. These results suggest that ammonium causes the inhibition of the assimilatory nitrate pathway, while nitrate exerts a positive effect. This pattern has been confirmed by RT-PCR. In the presence of both NO (3) (-) and NH (4) (+) , NH (4) (+) was preferentially consumed, but NO (3) (-) uptake was not completely inhibited by NH (4) (+) at prolonged time scale. The addition of MSX to NH (4) (+) or NO (3) (-) cultures results in an increase of Nas and NiR activities, suggesting that NH (4) (+) assimilation, rather than NH (4) (+ ) per se, has a negative effect on assimilatory nitrate reduction in Hfx. mediterranei.

Identification and transcriptional analysis of nitrate assimilation genes in the halophilic archaeon Haloferax mediterranei.

Sequencing a 6,720-bp segment of the extreme halophilic archaeon Haloferax mediterranei genome has revealed the genomic organization of the putative structural genes for nitrate assimilation. We report a gene operon containing nasABC and nasD gene. nasA encodes an assimilatory nitrate reductase, nasB codes for a membrane protein with similarity to the NarK transporter, nasC encodes a protein with similarity to MobA; and nasD codes for an assimilatory ferredoxin-dependent nitrite reductase. Reverse transcription-PCR and primer extension experiments have demonstrated the existence of one polycistronic messenger nasABC and one monocistronic nasD initiated from a different promoter. The gene order and the grouping in two adjacent transcriptional units constitutes a novel organization of nas genes. The promoter regions harbor direct palindromes reminiscent of target sites for binding of a hypotetical regulatory protein(s). Transcription of the nasABC and nasD regions was found to be repressed by the presence of ammonium as nitrogen source.

NMR studies of a ferredoxin from Haloferax mediterranei and its physiological role in nitrate assimilatory pathway.

Haloferax mediterranei is a halophilic archaeon that can grow in aerobic conditions with nitrate as sole nitrogen source. The electron donor in the aerobic nitrate reduction to ammonium was a ferredoxin. This ferredoxin has been purified and characterised. Air-oxidized H. mediterranei ferredoxin has a UV-visible absorption spectra typical of 2Fe-type ferredoxins with an A420/A280 of 0.21. The nuclear magnetic resonance (NMR) spectra of the ferredoxin showed similarity to those of ferredoxins from plant and bacteria, containing a [2Fe-2S] cluster. The physiological function of ferredoxin might be to serve as an electron donor for nitrate reduction to ammonium by assimilatory nitrate (EC 1.6.6.2) and nitrite reductases (EC 1.7.7.1). The apparent molecular weight (Mr) of the ferredoxin was estimated to be 21 kDa on SDS-polyacrylamide gel electrophoresis (SDS-PAGE).

Extreme halophilic enzymes in organic solvents.

The use of halophilic extremozymes in organic media has been limited by the lack of enzymological studies in these media. To explore the behaviour of these extremozymes in organic media, different approaches have been adopted, including the dispersal of the lyophilised enzyme or the use of reverse micelles. The use of reverse micelles in maintaining high activities of halophilic extremozymes under unfavourable conditions could open new fields of application such as the use of these enzymes as biocatalysts in organic media.

Mechanism of adaptation of an atypical alkaline p-nitrophenyl phosphatase from the archaeon Halobacterium salinarum at low-water environments.

Enzymes suspended in organic solvents represent a versatile system for studying the involvement of water in catalytic properties and their flexibility in adapting to different environmental conditions. The extremely halophilic alkaline p-nitrophenylphosphate phosphatase from the archaeon Halobacterium salinarum was solubilized in an organic medium consisting of reversed micelles of hexadecyltrimethylammoniumbromide in cyclohexane, with 1-butanol as cosurfactant. Hydrolysis of p-nitrophenylphosphate was nonlinear with time when the enzyme was microinjected into reversed micelles that contained substrate. These data are consistent with a kinetic model in which the enzyme is irreversibly converted from an initial form to a final stable form during the first seconds of the encapsulation process. The model features a rate constant (k) for that transition and separate hydrolysis rates, v(1) and v(2), for the two forms of the enzyme. The enzyme conversion may be governed by the encapsulation process.

Reverse micelles in organic solvents: a medium for the biotechnological use of extreme halophilic enzymes at low salt concentration.

Alkaline p-nitrophenylphosphate phosphatase (pNPPase) from the halophilic archaeobacterium Halobacterium salinarum (previously halobium) was solubilized at low salt concentration in reverse micelles of hexadecyltrimethyl-ammoniumbromide in cyclohexane with 1-butanol as co-surfactant. The enzyme maintained its catalytic properties under these conditions. The thermodynamic "solvation-stabilization hypothesis" has been used to explain the bell-shaped dependence of pNPPase activity on the water content of reverse micelles, in terms of protein-solvent interactions. According to this model, the stability of the folded protein depends on a network of hydrated ions associated with acidic residues at the protein surface. At low salt concentration and low water content (the ratio of water concentration to surfactant concentration; w0), the network of hydrated ions within the reverse micelles may involve the cationic heads of the surfactant. The bell-shaped profile of the relationship between enzyme activity and w0 varied depending on the concentrations of NaCl and Mn2+.

An extreme halophilic enzyme active at low salt in reversed micelles.

Possible biotechnological applications of extreme halophilic enzymes are strongly determined by their high salt requirement of around 4 M NaCl. Consequently, the use of these in organic media seemed to be unlikely. However, we have succeeded in dissolving a halophilic enzyme, p-nitrophenylphosphate phosphatase from the archaeon Halobacterium salinarum, in an organic medium by creating a reverse micellar system with very low salt concentration. The enzyme retained its catalytic properties in reversed micelles made with an anionic surfactant (dioctyl sodium sulphosuccinate) or with a cationic surfactant (hexadecyltrimethylammonium bromide) in cyclohexane plus 1-butanol as co-surfactant. The dependence of the rate of hydrolysis of p-nitrophenylphosphate phosphate on the molar water/surfactant ratio (w(0) value) showed a bell-shaped curve for each surfactant system. Kinetic parameters were determined in each system. The enzymatic reaction appeared to follow Michaelis-Menten kinetics with the anionic surfactant only. The kinetic behaviour was determined at different concentrations of Mn(2+) in reversed micelles of dioctyl sodium sulphosuccinate as surfactant.