Pseudomonas associated with Bursaphelenchus xylophilus,its insect vector and the host tree: A role in pine wilt disease?

In this study, we characterized the diversity of Pseudomonas associated with Bursaphelenchus xylophilus, its insect vector (Monochamus galloprovincialis) and its host (Pinus pinaster), by a culture‐independent approach using rpoD clone libraries. Clone libraries of Pseudomonas rpoD were obtained from B. xylophilus, M. galloprovincialis and infected P. pinaster. Most M. galloprovincialis and B. xylophilus sequences grouped together in the P. fluorescens group. Genes related to xenobiotics degradation and phenylacetate synthesis were present in the genomes of the type strains closely related to sequences retrieved from the nematode libraries. Results demonstrated that the nematode, during its life stages inside the tree, maintains a diverse Pseudomonas community that is closely related to the one associated with the insect vector. These bacteria might contribute to degradation of xenobiotics and tree weakening during the nematode tree infection.     

Machine learning methods for estimation the indicators of phosphogypsum influence in soil

Purpose

The full understanding of the effect of mineral waste-based fertilizer in soil is still unrelieved, because of the extreme complex chemical composition and plethora of their action pathways. The purposes of this paper is to quantify the input of PG into the soil ecosystem process, considering the direct effects of PG as a whole on soil environment using of a plethora of chemical, toxicological, and biological tests.

Materials and methods

Greenhouse experiment includes different PG doses (0, 1%, 3%, 7.5%, 15%, 25%, and 40%) and two-time collection points after treatments—7 and 28 days. For each treatment and each time collection point, we measure (i) soil pH, bioavailable (H₂0 and NH₄COOH-extractable) element content (S, P, K, Na, Mg, Ca, Fe, Zn, Sr, Ba, F); (ii) soil enzyme activities—dehydrogenase, urease, acid phosphatase, FDA; (iii) soil CO₂ respiration activity with and without glucose addition; (iv) Eisenia fetida, Sinapis alba, and Avena sativa responses. Finally, we combine the ordinary chemical, toxicology, and biological measuring of soil properties with state-of-the-art mathematical analysis, namely (i) support vector machines (used for prediction), (ii) mutual information test (variable importance tasks), (iii) t-SNE and LLE algorithms (used for unsupervised classification).

Results and discussion

The results show similarity between the 0%, 1%, and 3% PG treatments in all collection times based on the toxicological and biological properties. Beyond 7.5% PG, some biological test was significantly inhibited in response to trace element stress. Among all tested parameters, soil urease activities, soil respiration activities after glucose addition, S. alba root lengths, and E. fetida survival rates show sensitivity to PG addition. Furthermore, the machine learning algorithms revealed that only several elements (mobile and water-soluble forms of Ca, Ba, Sr, S, and Na; water-soluble F) could be responsible to elevated soil toxicity for those indicators. SVR models were able to predict soil biological and ecotoxicity properties, and increasing numbers of randomly selected training examples from 50 to 90% of initial experimental data significantly improved model performance.

Conclusions

At this study, we demonstrate benefits of unsupervised machine learning methods for investigating toxicity of man-made substances in soil that can be further applied to risk assessments of various toxins, which are of significant interest to environmental protection.

     

Biodegradation of humic substances by microscopic filamentous fungi: chromatographic and spectroscopic proxies

Purpose

The study of interactions between humic substances (HSs) and soil filamentous fungi is the key to understanding the sustainable soil functioning. The present work aims to examine the decomposition of HSs by filamentous dark-pigmented fungus Alternaria alternatа under the laboratory conditions and to determine the effect of easily assimilable organic carbon on this process. Analyzing such polydisperse substances like HSs by a complex integrated methodology makes it possible to explore the data on their decomposition by microorganisms.

Materials and methods

To achieve the aforementioned goals, we used chromatographic and spectroscopic approaches: low-pressure size-exclusion and hydrophobic interaction chromatography accompanied by absorption and fluorescence spectroscopy. To determine the effect cometabolism conditions produced on HS decomposition, two types of carbon substrates were added to the nutrient media: easily assimilable organic carbon (standard 0.3% or reduced 0.03% sucrose content) and hardly assimilable organic carbon (HSs), as well as their combinations. Five HS samples of different organic matter origin have been inspected: potassium humates (HPs) and humic acids (HAs) from coal, peat, and lignosulfonate. Correlation matrix and principal component analysis (PCA) were calculated for comprehensive data analysis.

Results and discussion

Transformations of the investigated HSs under fungal cultivation lead to the increase in the low molecular weight fraction, rise of hydrophilic fraction, enlargement of absorbance ratio A₂₅₀/A₃₆₅, shortening of the emission wavelength of the humic-type fluorescence, and growth in the fluorescence quantum yield measured with excitation at 355 nm. A positive correlation was observed between the accumulation of fungal biomass and the degree of HS decomposition. PCA analysis confirms that the difference in the results of HS decomposition largely depends on the sucrose content and the nature of HSs. We divided all the HS samples into four groups according to the degree of HS decomposition: original HS solutions, HPs altered using fungal cultivation at 0.03% sucrose, HAs after fungal cultivation at 0.03% sucrose, and finally, HSs (both HPs and HAs) after fungal cultivation at 0.3% sucrose.

Conclusions

In the laboratory experiments, we showed that (1) the isolated HAs were more effectively degraded than the parent HPs, and this process was more pronounced at a reduced sucrose content, and (2) the decomposition of stable organic compounds (HSs) was activated by the easily assimilable carbon sources (especially 0.3% sucrose) being present. We assume that it is the easily assimilable organic carbon that most likely triggers the HS degradation working as the priming effect in natural environments.

     

Extreme neutral genetic and morphological divergence supports classification of Adriatic three-spined stickleback (Gasterosteus aculeatus) populations as distinct conservation units

The fact that the intraspecific genetic differentiation in neutral genetic markers and genes coding for adaptive traits are not typically correlated has caused a great deal of conceptual and practical trouble in delimitation of conservation units. Although the importance of combining information on adaptive genetic divergence with information on historical and recent gene flow in the delimitation of conservation units has been recognized, integrated empirical studies to this end are still rare. We explored the evidence for the specific conservation status of two freshwater three-spined stickleback (Gasterosteus aculeatus) populations on the Adriatic side of the Balkan Peninsula by comparing their phenotypic and genetic characteristics to those of other representative European populations. Apart from focusing on the neutral genetic divergence in mitochondrial DNA sequences and microsatellite markers, we also compared the patterns of morphological differentiation (i.e. bony armour development) resulting from adaptation to freshwater environments. The Balkanic populations formed two distinct groups with regard to neutral genetic variation and had the least developed bony armour of all the examined populations. All morphometric analyses identified the two Balkanic populations as phenotypically – and hence most likely also ecologically – clearly distinct from other European three-spined stickleback populations. These results suggest that the two Balkanic populations (River Neretva and River Zeta) fulfil the most stringent criteria (i.e. lack of genetic and ecological exchangeability) to be classified as conservation units distinct from other European three-spined stickleback populations.     

Nutrient solution monitoring in greenhouse cultivation employing a potentiometric electronic tongue

This work investigates the use of electronic tongues for monitoring nutrient solution compositions in closed soilless systems. This is a horticultural technique in which the nutrient solution is continuously recirculated and an automatic recomposition system maintains the concentration of the different ions in the optimum range for the plants. Electronic tongues used in this study comprised an array of potentiometric sensors and complex data processing by artificial neural networks. A first experiment was able to carry out the simultaneous inline monitoring of ammonium, potassium, sodium, chloride, and nitrate ions during the winter. In the second and third applications, done during summer, some changes were introduced in the sensor array to improve its response toward chloride ions and to incorporate phosphate in the model. This electronic tongue was validated with real greenhouse samples and was also able to detect the variations in the ion concentrations caused by an incorrect configuration of the recomposition system.     

Drying of Pedro Ximenez grapes in chamber at controlled temperature and with dipping pretreatments. Changes in the color fraction

The drying of Pedro Ximenez grapes in chamber at a controlled temperature of 40 or 50 degrees C is studied. Compared to traditional sun-drying, the chamber-drying shortened the drying time by about 40% at 50 degrees C. In color terms, the musts obtained from grapes dried at 50 degrees C were closer in CIELab coordinates to those obtained by sun-dried grapes, with similar h(ab) values and slightly lower L* and C(ab)*. To shorten further the drying times at 50 degrees C, the grapes were dipped in olive oil or ethyl oleate emulsions containing potassium carbonate. The ethyl oleate pretreatment shortened additionally the drying time by about 25%, providing musts with chroma, lightness, and hue similar to those without grape pretreatment. In general, except for the phenolic compounds corresponding to the drying with ethyl oleate pretreatment, most of these compounds in the remainding conditions studied increased to a lesser extent than expected because of water losses of the grapes during drying, revealing degradation reactions.     

Enzymatic treatment to improve extraction of capsaicinoids and carotenoids from chili (Capsicum annuum) fruits

Enzymatic treatments using noncommercial enzymes as a means to the improve the extraction of carotenoids and capsaicinoids from chili fruits are explored in this study. The results show that it is possible to obtain chili fruit powder with a higher concentration of both capsaicinoids and carotenoids than previously reported for similar processes. Furthermore, extraction yields above 96% for carotenoids and 85% for capsaicinoids as separate fractions can be achieved using a sequential and selective two-stage extraction. Evidence is presented demonstrating that the content and extraction yield depend directly on the extent of the enzymatic hydrolysis of chili cell walls, and higher yields are obtained when the sample is completely hydrolyzed. The enzymatic treatment described here is a promising alternative to current industrial practices, and it improves the extraction of carotenoids and capsaicinoids from chili fruits.     

Optimization of color and antioxidant activity of peach and nectarine puree: scale-up study from pilot to industrial plant

The effects of an innovative process for the manufacture of peach and nectarine purees on the main quality indices, namely, color, consistency, carotenoid and phenolic content, and antioxidant activity, were studied using a peach cultivar that is optimal for nectar processing (cv. Redhaven) and peach and nectarine varieties that undergo a faster browning degradation. The innovative process, operating the pulping/finishing step at room temperature, was compared to the traditional process of hot pulping/finishing. The study comprised initial trials on a pilot plant scale and scaling up to industrial production of the puree and nectar. The quality of products was analyzed at the time of production and as a function of storage of both the puree and the nectar. With respect to the traditional process, the new process, scaled up to industrial levels, improved the color of peach and nectarine products (by increasing the L* value and decreasing the a* value), whatever the variety studied; maintained almost the same levels of carotenoids, hydroxycinnamates, flavan-3-ols, and flavonols; and reduced the level of cyanidin 3-O-glucoside. The presence of cyanidin 3-O-glucoside was correlated to an unstable and undesirable red hue of the products (even if its concentration was very low in all products), and the decreased level obtained by the innovative process was considered to be positive. On the basis of these results, new technology can be proposed for the processing of fruit varieties that are not suitable for puree production using traditional technology. This opens up two possibilities: (a) utilization of fresh market fruit surplus and (b) processing of selected fruit varieties that are rich in antioxidants but have a high browning potential, such as the Stark Red Gold nectarine. Furthermore, as the positive impact of the new technology is optimal at the beginning of storage, it is particularly suitable for fruit-based products with a short shelf life.     

Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail)

Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides.     

Nutritional Contribution of Biofloc within the Diet of Growout and Broodstock of Litopenaeus vannamei,Determined by Stable Isotopes and Fatty Acids

The relative contributions of feed sources were determined through the isotopic signal (δ¹³C and δ¹⁵N) and fatty acid profile of feed items, shrimp muscle, and eggs of Litopenaeus vannamei reared in a biofloc system. In the growout phase, the isotope analysis showed the biofloc particle size class ≥250 μm contributed 55–100%; size ≥50 < 250 μm contributed 0–22%; and artificial feed contributed 0–45%. Principal component analysis applied to fatty acid profiles showed that biofloc ≥250 μm and artificial feed were the most important items in shrimp growout. For the egg production, isotope analysis suggested that the most important feed sources according to their relative contributions were polychaetes (0–100%), followed by artemia biomass (0–86%) and semi‐moist feed (0–66%), with lower contributions from squid, mussel, and the muscle of L. vannamei broodstock that had been cultured in biofloc. In terms of fatty acids, the most important items were artemia, polychaetes, and semi‐moist feeds. This work clarified the importance of feed sources for shrimp during culture in biofloc systems and during reproduction. Analysis of stable isotopes and fatty acids can be successfully used to trace the assimilation of nutrients during the nutrition of shrimp.