Exploration,antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran

In the present study, halophilic bacteria communities were explored in saline soils of Howze-Soltan playa in Iran with special attention to their biological activity against an aflatoxigenic Aspergillus parasiticus NRRL 2999. Halophilic bacteria were isolated from a total of 20 saline soils using specific culture media and identified by 16S rRNA sequencing in neighbor-joining tree analysis. Antifungal and antiaflatoxigenic activities of the bacteria were screened by a nor-mutant A. parasiticus NRRL 2999 using visual agar plate assay and confirmed by high-performance liquid chromatography. Among a total of 177 halophilic bacteria belonging to 11 genera, 121 isolates (68.3%) inhibited A. parasiticus growth and/or aflatoxin production. The most potent inhibitory bacteria of the genera Bacillus, Paenibacillus and Staphylococcus were distributed in three main phylogenetic clusters as evidenced by 16S rRNA sequence analysis. A. parasiticus growth was inhibited by 0.7–92.7%, while AFB₁ and AFG₁ productions were suppressed by 15.1–98.9 and 57.0–99.6%, respectively. Taken together, halophilic bacteria identified in this study may be considered as potential sources of novel bioactive metabolites as well as promising candidates to develop new biocontrol agents for managing toxigenic fungi growth and subsequent aflatoxin contamination of food and feed in practice.

     

A systematic survey of centrality measures for protein-protein interaction networks

Background

Numerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.

Results

We used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.

Conclusions

The choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

     

Combined or Individual Effects of Dietary Probiotic <Emphasis Type="Italic">Pedicoccus acidilactici</Emphasis> and Nucleotide on Growth Performance,Intestinal Microbiota,Hemato-biochemical Parameters,and Innate Immune Response in Goldfish (<Emphasis Type="Italic">Carassius auratus</Emphasis>)

This study investigated the effect of dietary supplementation of probiotic Pedicoccus acidilactici and nucleotide (separately or combined) on growth performance, intestinal microbiota, hemato-immunological parameters, and immunity response in goldfish (Carassius auratus). Fish (average weight 5–6 g) were acclimatized and divided into eight experimental diets supplemented with P. acidilactici of different concentrations (0.1, 0.2, and 0.3% diet) and nucleotides (0 and 0.5% diet) for 6 months. Fish fed with experimental diets showed significant differences in terms of final weight, weight gain, feed conversion ratio, daily growth rate, and condition factor when compared to control diet (P < 0.05). Fish fed with probiotic (0.3%) separately and combined with nucleotide (0.5%) had highest RBC and WBC when compared to other diets (P < 0.05), while the highest values for Hb and Hct as well as total protein, glucose, albumin, and globulin were observed in probiotic (0.2%) and nucleotide (0.5%) combined diet. Serum lysozyme and anti-protease activities were significantly higher in probiotic (0.1 and 0.2%) and nucleotide (0.5%) combined diets. Similarly, these two diets combined showed the highest colonization of P. acidilactici when compared to other diets. In conclusion, combined dietary probiotic and nucleotide improve the growth performance, hemato-biochemical parameters, and intestine growth in C. auratus.     

Application of zeolite and geohumus superabsorbent on establishment and some growth indices of Nitraria schoberi L.

Using Superabsorbent is one of the solutions to water shortages in arid and semi-arid regions. In order to evaluate the effect of zeolite and geohumus on the growth of Nitraria schoberi L. species, a factorial experiment in a completely randomized design was conducted with nine replications in Kashan city. The treatments consisted of various zeolite levels (0, 10 and 15 wt%) and geohumus (0, 100, 150, 250 gr for hole) and irrigation (normal irrigation, low irrigation). This study showed that superabsorbent application has a positive effect on establishment and other indices such as plant height, large and small canopy diameter and collar diameter. The highest survival percentage was observed in superabsorbent application (100%) and the lowest was measured in control treatment of low irrigation (the soil free of modifying substances) (78%). Also, the most growth indices of the plant are related to the treatment of 250 g geohumus with low irrigation treatment. Based on the results, it was found that adding superabsorbent on soil causes more establishment and improves vegetative growth traits. Also, considering the economical price of zeolite superabsorbent compared to geohumus as well as its abundance in Iran, it is recommended to use in order to increase irrigation intervals and reduce costs in desertification projects.     

Suitability of dried herbarium specimens for NMR metabolomics of mushrooms. A comparison of four species of the genera Kuehneromyces and Hypholoma (Strophariaceae)

Herbarium specimens are a treasure trove for biochemical studies. However, this implies understanding of the chemical changes during the drying and storage of the specimen. We compared herbarium specimens at different ages and fresh samples of four mushroom species (Kuehneromyces mutabilis, Hypholoma capnoides, Kuehneromyces lignicola, Hypholoma fasciculare) of two genera in the family Strophariaceae by using proton nuclear magnetic resonance (¹H NMR) spectroscopy combined with principal component analysis (PCA). 25 metabolites were identified. No significant alterations were found between herbarium samples at different ages, suggesting that they are stable enough for comparative studies. The most dominant differences between fresh and herbarium samples was that sugars such as α-α-trehalose, and fumaric and malic acids were more abundant in fresh fungi. Total contents of fatty and amino acids, uracil and γ-aminobutyric acid (GABA) were higher in herbarium specimens. In addition, pyroglutamic acid was observed only in Kuehneromyces mutabilis and fasciculic acid E in Hypholomafasciculare. Hence, based on results of the studied taxa, we conclude that NMR metabolomics can be used for both fresh and dried mushrooms when such alterations are properly addressed.     

Sesame genotype influences growth and phenology of Phelipanche aegyptiaca

Egyptian broomrape (Phelipanche aegyptiaca) is a parasitic weed causing major yield loss in many field and vegetable crops. Recent observations in Iran suggest that sesame (Sesamum indicum) may serve either as a trap crop or as a host for broomrape, depending on genotype. The central objective of this research was to identify sesame genotypes that could act either as potential trap crops, or sources of genetic material for development of broomrape resistant cultivars. Seeds of 11 Iranian sesame genotypes (Ardestan, Esfarayen, Oltan, Ahvaz, Borazjan, Darab‐14, Ferdous, Kalat, Naz Tak Shakhe, Varamin and Yekta) and 10 foreign genotypes (S16, S21, S23, S25, S4, S5, S6, S7, S8 and S9) were planted with broomrape seeds in pots. At the flowering stage of sesame, tubercle number and dry weight, shoot number and dry weight and shoot height of broomrape were determined. Shoot dry weight, root dry weight and seed yield of sesame were determined at the physiological maturity. The results showed that broomrape growth varied with sesame genotype. Egyptian broomrape dry weight measured from 1.6% (S23) to 35.4% (Kalat) of the dry weight of the sesame on which it grew. Broomrape total dry weight had positive and highly correlation with the root dry weight of the sesame genotype on which it grew. When broomrape planted with the S7, S8, S9, S21 and S23 genotypes produced tubercles, but no shoots on these genotypes. Such genotypes could be used as both trap crops and as breeding‐sources for development of resistant sesame genotypes.     

Biodegradation perspectives of azo dyes by yeasts

Azo dyes are the largest class of synthetic dyes, which are widely used in the textile industry. The amount of dyestuff does not bind to the fibers and is lost in wastewater during textile processing. The discharge of colored effluents into the environment is not only aesthetically unpleasing. Moreover, dyes and their break-down products cause toxic effects and they affect photosynthetic activity of aquatic systems by reducing light penetration. A number of microorganisms belonging to different taxonomic groups of bacteria, algae, fungi and yeast have been reported for their ability to decolorize azo dyes. In the literature the ability to decolorize azo dyes by yeasts, compared to bacterial and fungal species, has been studied in a few reports. Within this review, an attempt is made to elucidate some basic biological aspects associated with the azo dye degradation by yeasts and enzymes involved that are responsible for degradation process.