Antioxidant activity and phenolic profile of pistachio (Pistacia vera L., variety Bronte) seeds and skins

Pistachio (Pistacia vera L.; Anacardiaceae) is native of aride zones of Central and West Asia and distributed throughout the Mediterranean basin. In Italy, a pistachio cultivar of high quality is typical of Bronte (Sicily), an area around the Etna volcano, where the lava land and climate allow the production of a nut with intense green colour and aromatic taste, very appreciated in international markets. Pistachio nuts are a rich source of phenolic compounds, and have recently been ranked among the first 50 food products highest in antioxidant potential. Pistachio nuts are often used after removing the skin, which thus represents a significant by-product of pistachio industrial processing. The present study was carried out to better characterize the phenolic composition and the antioxidant activity of Bronte pistachios, with the particular aim to evaluate the differences between pistachio seeds and skins. The total content of phenolic compounds in pistachios was shown to be significantly higher in skins than in seeds. By HPLC analysis, gallic acid, catechin, eriodictyol-7-O-glucoside, naringenin-7-O-neohesperidoside, quercetin-3-O-rutinoside and eriodictyol were found both in pistachio seeds than in skins; furthermore, genistein-7-O-glucoside, genistein, daidzein and apigenin appeared to be present only in pistachio seeds, while epicatechin, quercetin, naringenin, luteolin, kaempferol, cyanidin-3-O-galactoside and cyanidin-3-O-glucoside are contained only in pistachio skins. The antioxidant activity of pistachio seeds and skins were determined by means of four different assays (DPPH assay, Folin-Ciocalteau colorimetric method and TEAC assay, SOD-mimetic assay). As expected on the basis of the chemical analyses, pistachio skins have shown to possess a better activity with respect to seeds in all tests. The excellent antioxidant activity of pistachio skins can be explained by its higher content of antioxidant phenolic compounds. By HPLC-TLC analysis, gallic acid, catechin, cyanidin-3-O-galactoside, eriodictyol-7-O-glucoside and epicatechin appeared to be responsible for the antioxidant activity of pistachio skin, together with other unidentified compounds. In conclusion, our work has contributed to clarify some particular characteristics of Bronte pistachios and the specific antioxidant power of pistachio skins. Introduction of pistachios in daily diet may be of undoubted utility to protect human health and well-being against cancer, inflammatory diseases, cardiovascular pathologies and, more generally, pathological conditions related to free radical overproduction. On the other hand, pistachio skins could be successfully employed in food, cosmetic and pharmaceutical industry.     

Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov

In a survey of rhizobia associated with the native legumes in Yunnan Province, China, seven and nine strains isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and Medicago lupulina were respectively classified into the novel genomic species groups I and II in the genus Ensifer (former Sinorhizobium) based on the sequence analyses of the 16S rRNA gene. Analyses of concatenated housekeeping genes (atpD, recA and glnII) further revealed that they were distinct lineages in the genus, and group I was most similar to Ensifer terangae and Ensifer garamanticus (both with 94.2% similarity), while group II was most similar to Ensifer adhaerens (94.0%). These groups could be distinguished from closely related species by DNA–DNA relatedness, MALID-TOF MS, cellular fatty acid profiles and a series of phenotypic characters. Therefore, two novel species were proposed: Ensifer psoraleae sp. nov. (seven strains, type strain CCBAU 65732^T = LMG 26835^T = HAMBI 3286^T) and Ensifer sesbaniae sp. nov. (nine strains, type strain CCBAU 65729^T = LMG 26833^T = HAMBI 3287^T). They had a DNA G + C mol% (T_m) of 58.9 and 60.4, respectively. Both of the type strains formed effective nodules on common bean (Phaseolus vulgaris) and their hosts of origin. In addition, the previously described species Sinorhizobium morelense and Sinorhizobium americanum were renamed as Ensifer morelense comb. nov. and Ensifer americanum comb. nov. according to the accumulated data from different studies.     

Vibrio celticus sp. nov., a new Vibrio species belonging to the Splendidus clade with pathogenic potential for clams

A group of four motile facultative anaerobic marine isolates (Rd 8.15^T [=CECT 7224^T, =LMG 23850^T], Rd 16.13, Rd 6.8 [=LMG 25696] and Rd2L5) were obtained from cultured clams (Ruditapes philippinarum and Venerupis pullastra) in Galicia, north-western Spain. They formed a tight phylogenetic group based on sequences of the 16S rRNA gene and the four housekeeping genes rpoA (encoding the α-chain of RNA polymerase), rpoD (encoding the sigma factor of RNA polymerase), recA (encoding RecA protein), and atpA (encoding the α-subunit of bacterial ATP synthase). The phylogenies based on these sequences indicated that the four isolates represented a novel species in the genus Vibrio, and more precisely in the Splendidus clade. DNA–DNA hybridizations with the type strains of species showing more than 98.6% 16S rRNA gene sequence similarity, revealed a DNA–DNA relatedness below 70%. The isolates could be differentiated from the phylogenetically related Vibrio species on the basis of several phenotypic features. In addition, strain Rd 8.15^T showed potential pathogenic activity for adult clams in virulence assays. The name Vibrio celticus sp. nov. is proposed for this new taxon, with the type strain being Rd 8.15^T (=CECT 7224^T, =LMG 23850^T).     

Purification and characterization of Xanthomonas campestris pv. glycines exopolysaccharide

The exopolysaccharides (EPS) of virulent and avirulent strains of Xanthomonas campestris pv. glycines, causal agent of bacterial pustule disease of soybean, and one strain of the soybean non-pathogen X. c. pv. campestris were isolated, purified, and their compositions compared. EPS produced by X. c. pv. glycines in a completely defined medium appears to be identical to the well-characterized EPS produced by X. c. pv. campestris (commonly referred to as xanthan gum). The EPS of all strains was composed of the carbohydrates glucose, mannose and glucuronic acid with acetyl and pyruvyl substituents present. Permethylation analyses indicated EPS preparations had identical hexose substitution patterns. Avirulent strains of X. c. pv. glycines produced as much or more acidic EPS as did virulent strains in vitro. None of the EPS preparations were active as elicitors of the soybean pterocarpanoid phytoalexin glyceollin as determined by a soybean cotyledon bioassay.     

Seminibacterium arietis gen. nov., sp. nov., isolated from the semen of rams

Two gram-negative, catalase- and oxidase-positive, bacillus-shaped bacterial strains were isolated from the semen of two rams. 16S rRNA gene sequencing demonstrated that both isolates represented a distinct subline within the family Pasteurellaceae with <95% sequence similarity to any recognized member of this family. Sequencing of rpoB and infB genes confirmed this finding with the semen isolates representing a new sub-line within the family Pasteurellaceae. The main cell fatty acids of strain DICM-00342^T were C_14:0, C_16:0, C_18:1ω7c and summed feature 3 (C_16:1ω7c/iso-C_15:0 2OH). Ubiquinone Q-8 was the major quinone and 1,3-diaminopropane was the predominat polyamine. Major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The new genus can be phenotypically distinguished from currently described genera of this family based on physiological traits and a combination of signature amino acids in the RpoB protein sequence. On the basis of these results we describe a new genus and species for which we propose the name of Seminibacterium arietis gen. nov., sp. nov. (DICM11-00342^T = CCUG 61707^T = CECT 8033^T).     

Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov., isolated from the preen glands of Great Spotted Woodpeckers (Dendrocopos major)

Two new species of Gram-positive cocci were isolated from the uropygial glands of wild woodpeckers (Dendrocopos major) originating from different locations in Germany. A polyphasic approach confirmed the affiliation of the isolates to the genus Kocuria. Phylogenetic analysis based on the 16S rRNA gene showed high degree of similarity to Kocuria koreensis DSM 23367^T (99.0% for both isolates). However, low ANIb values of <80% unequivocally separated the new species from K. koreensis. This finding was further corroborated by DNA fingerprinting and analysis of polar lipid profiles. Furthermore, growth characteristics, biochemical tests, MALDI-TOF MS analysis, and G + C contents clearly differentiated the isolates from their known relatives. Besides, the woodpecker isolates significantly differed from each other in their whole-cell protein profiles, DNA fingerprints, and ANIb values. In conclusion, the isolated microorganisms constitute members of two new species, for which the names Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov. are proposed. The type strains are 36^T (DSM 101740^T = LMG 29265^T) and 257^T (=DSM 101741^T = LMG 29266^T) for K. uropygialis sp. nov. and K. uropygioeca sp. nov., respectively.     

Hexasaturnalis nakasekoi nov. sp., a Jurassic saturnalid radiolarian species frequently confounded with Hexasaturnalis suboblongus (Yao)

Detailed morphological study of the ring of the Jurassic saturnalid radiolarian species frequently cited in the literature as Hexasaturnalis suboblongus (Yao) has proven that it contains two well-defined species: H. suboblongus (Yao), practically ranging within the boundaries of the Bajocian, and Hexasaturnalis nakasekoi nov. sp., ranging within the Bathonian-Kimmeridgian interval. The two species seem to be important stratigraphically because the transition from the former to the latter took place at or around the Bajocian/Bathonian boundary. The phyletic lineage Hexasaturnalis hexagonus (Yao) → H. inuyamaensis (Yao) → H. suboblongus (Yao) → H. nakasekoi nov. sp. → H. minor (Baumgartner) → Dicerosaturnalis angustus (Baumgartner) → D. dicranacanthos (Squinabol) is proposed.     

Antioxidant metabolism of grapefruit infected with Xanthomonas axonopodis pv. citri

Grapefruit is one of the most susceptible citrus genotypes to Asiatic Citrus Canker, caused by Xanthomonas axonopodis pv. citri (Xac), that can cause severe losses in citrus yield and quality. Although much is known about citrus response to Xac, little is known of the role of antioxidant metabolism. Grapefruit leaves were artificially injected with a strain of Xac obtained from a commercial grove in Florida and components of oxidative metabolism were measured. Symptoms observed included water soaking (2 dai; days after inoculation), raised and ruptured epidermis (6-8 dai), formation of necrotic lesions (16 dai), and leaf abscission (21 dai). The Xac population increased to a maximum (≈10⁹ CFU/cm²) 8 dai and then declined to ≈10⁷ CFU/cm² by 20 dai. Lipid peroxidation was higher in infected leaves than uninoculated controls from 4 to 21 dai indicating greater oxidative stress. H₂O₂ concentration demonstrated a biphasic pattern with peak concentrations at 4 and 13 dai and minimum concentrations that were lower than the controls at 10 and 20 dai. The H₂O₂ concentration somewhat corresponded with superoxide dismutase (SOD) activity, which generates H₂O₂ via dismutase of superoxide ions. Total SOD activity in Xac-infected leaves increased to a maximum at 4 dai, the day of highest H₂O₂ concentration, and then declined and remained at or below controls. Mn-SOD and Fe-SOD activities both increased to maximum activities at 4 dai. Mn-SOD had four isoforms in Xac-infected leaves but only three in the controls. Fe-SOD had three isoforms in both infected and control plants. Suppression of H₂O₂ in Xac-infected leaves also corresponded to higher activities of the H₂O₂ catabolising enzymes catalase (CAT), ascorbate peroxidase (APOD), and peroxidase (POD). Two additional CAT isoforms were detected in infected leaves and not the controls. Three POD isoforms were detected in both control and infected leaves. Previous research has shown that Xac is sensitive to intraplant H₂O₂ concentration, however, the pattern of Xac in this study did not correspond to H₂O₂ concentration, which initially increased due to enhanced SOD activity, but was later suppressed apparently with the aid of peroxidases. In conclusion, Xac infection altered H₂O₂ metabolism in grapefruit leaves by changes in the activities and isoforms of SODs, CATs, PODs and APOD.     

Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

The plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight, which is one of the most serious diseases of rice. Xoo has been studied for over one century, and much has been learned about it, but proteomic investigation has been neglected. In this study, proteome reference maps of Xoo were constructed by two-dimensional gel electrophoresis, and 628 spots in the gels representing 469 different protein species were identified with MALDI-TOF/TOF MS. The identified spots were assigned to 15 functional categories according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the annotations from the National Center for Biotechnology Information (NCBI) database. The data set has been deposited in the World-2DPAGE database (Database ID: 0044). In addition, comparative proteomic analysis revealed that proteins related to the TonB-dependent transportation system and energy metabolism are involved in the phenazine-1-carboxylic acid resistance in Xoo. In conclusion, we have established a proteome database for Xoo and have used this database in a comparative proteomic analysis that identified proteins potentially contributing to phenazine-1-carboxylic acid resistance in Xoo.     

Proposal of Lysobacter pythonis sp. nov. isolated from royal pythons (Python regius)

The bacterial strains 4284/11T and 812/17 isolated from the respiratory tract of two royal pythons in 2011 and 2017, respectively were subjected to taxonomic characterization. The 16S rRNA gene sequences of the two strains were identical and showed highest sequence similarities to Lysobacter tolerans UM1^T (97.2%) and Luteimonas aestuarii DSM 19680^T (96.7 %). The two strains were identical in the sequences of the 16S-23S rRNA internal transcribed spacer (ITS) and partial groEL gene sequences and almost identical in genomic fingerprints. In the ITS sequence Ly. tolerans DSM 28473^T and in the groEL nucleotide sequence Luteimonas mephitis DSM 12574^T showed the highest similarity. In silico DDH analyses using genome sequence based ANIb and gANI similarity coefficients demonstrated that strain 4284/11^T represents a novel species and revealed Ly. tolerans UM1^T as the next relative (ANIb = 76.2 %, gANI = 78.0 %). Based on the topology of a core gene phylogeny strain 4284/11^T could be assigned to the genus Lysobacter. Chemotaxonomic characteristics including polyamine pattern, quinone system, polar lipid profile and fatty acid profile were in accordance with the characteristics of the genera Lysobacter and Luteimonas. Strains 4284/11^T and 812/17 could be differentiated from the type strains of the most closely related species by several physiological tests. In conclusion we are here proposing the novel species Lysobacter pythonis sp. nov. The type strain is 4284/11^T (= CCM 8829^T = CCUG 72164^T = LMG 30630^T) and strain 812/17 (CCM 8830) is a second strain of this species.     

Definition of a novel symbiovar (sv. retamae) within Bradyrhizobium retamae sp. nov., nodulating Retama sphaerocarpa and Retama monosperma

In this paper we analyze through a polyphasic approach several Bradyrhizobium strains isolated in Spain and Morocco from root nodules of Retama sphaerocarpa and Retama monosperma. All the strains have identical 16S rRNA genes and their closest relative species is Bradyrhizobium lablabi CCBAU 23086^T, with 99.41% identity with respect to the strain Ro19^T. Despite the closeness of the 16S rRNA genes, the housekeeping genes recA, atpD and glnII were divergent in Ro19^T and B. lablabi CCBAU 23086^T, with identity values of 95.71%, 93.75% and 93.11%, respectively. These differences were congruent with DNA–DNA hybridization analysis that revealed an average of 35% relatedness between the novel species and B. lablabi CCBAU 23086^T. Also, differential phenotypic characteristics of the new species were found with respect to the already described species of Bradyrhizobium. Based on the genotypic and phenotypic data obtained in this study, we propose to classify the group of strains isolated from R. sphaerocarpa and R. monosperma as a novel species named Bradyrhizobium retamae sp. nov. (type strain Ro19^T = LMG 27393^T = CECT 8261^T). The analysis of symbiotic genes revealed that some of these strains constitute a new symbiovar within genus Bradyrhizobium for which we propose the name “retamae”, that mainly contains nodulating strains isolated from Retama species in different continents.     

Phenotypic, molecular phylogenetic, and pathogenetic characterization of Fusarium crassistipitatum sp. nov., a novel soybean sudden death syndrome pathogen from Argentina and Brazil

A novel soybean sudden death syndrome (SDS) pathogen from Argentina and Brazil is formally described herein as Fusarium crassistipitatum based on detailed phenotypic analyses of macro- and microscopic characters and phylogenetic analyses of multilocus DNA sequence data. Fusarium crassistipitatum can be distinguished from the other soybean SDS and bean (Phaseolus/Vigna) root rot pathogens (BRR) phenotypically by the production of yellowish colonies on PDA; and tall, stout, and mostly unbranched conidiophores with a thick-walled base, which form multiseptate conidia apically. Phylogenetic species recognition based on genealogical concordance of a six-gene dataset strongly supported the reciprocal monophyly of F. crassistipitatum with respect to the other SDS and BRR pathogens. Isolates of F. crassistipitatum were able to induce typical SDS foliar and root rot symptoms on soybean that were indistinguishable from those caused by three other SDS pathogens (i.e., F. virguliforme, F. brasiliense, and F. tucumaniae) on susceptible cultivars A-6445RG and N-4613RG in a pathogenicity experiment.     

Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium

A new ethylenediaminetetraacetic acid (EDTA)-utilizing gammaproteobacterial strain LPM-5^T was isolated from municipal sewage sludge. Aerobic, gram-negative, motile rods multiply by binary fission. Neutrophilic and mesophilic, these are unable to grow in the presence of 3% NaCl (w/v), and unable to reduce nitrate to nitrite, and are oxidase and catalase positive, but lipase negative. The major cellular fatty acids are C_i15:0, C_a15:0 and C_16:1w7c. The dominant phospholipids are phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.3 mol% (T_m). The 16S rRNA gene sequence analysis showed a high similarity of strain LPM-5^T to the species members of genus Stenotrophomonas: S. maltophilia LMG 958^T (98.6%), S. rhizophila CCUG 47042^T (98.3%), S. koreensis TR6-01^T (97.6%) and S. acidaminiphila CIP 106456^T (97.0%). Based on these results and modest DNA–DNA hybridization levels with S. maltophilia VKM B-591^T (=LMG 958^T) (51%) and S. rhizophila CCUG 47042^T (52%), the isolate was classified as a novel species, Stenotrophomonas chelatiphaga sp. nov. (type strain LPM-5^T=VKM B-2486=DSM-21508=CCUG 57178).     

Suttonium praedicator nov. gen., nov. sp. (radiolaria,nassellaria) et la famille des Suttonidae nov. fam.

The peculiar morphology of the abdomen from a new radiolaria of the south-equatorial Pacific Ocean allows us to create a new family.     

Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples

The phenotypic and genotypic characteristics of fourteen human clinical Achromobacter strains representing four genogroups which were delineated by sequence analysis of nusA, eno, rpoB, gltB, lepA, nuoL and nrdA loci, demonstrated that they represent four novel Achromobacter species. The present study also characterized and provided two additional reference strains for Achromobacter ruhlandii and Achromobacter marplatensis, species for which, thus far, only single strains are publicly available, and further validated the use of 2.1% concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequence divergence as a threshold value for species delineation in this genus. Finally, although most Achromobacter species can be distinguished by biochemical characteristics, the present study also highlighted considerable phenotypic intraspecies variability and demonstrated that the type strains may be phenotypically poor representatives of the species. We propose to classify the fourteen human clinical strains as Achromobacter mucicolens sp. nov. (with strain LMG 26685^T [=CCUG 61961^T] as the type strain), Achromobacter animicus sp. nov. (with strain LMG 26690^T [=CCUG 61966^T] as the type strain), Achromobacter spiritinus sp. nov. (with strain LMG 26692^T [=CCUG 61968^T] as the type strain), and Achromobacter pulmonis sp. nov. (with strain LMG 26696^T [=CCUG 61972^T] as the type strain).     

Three new asexual arthroconidial yeasts, Geotrichum carabidarum sp. nov., Geotrichum histeridarum sp. nov., and Geotrichum cucujoidarum sp. nov., isolated from the gut of insects

Twenty arthroconidial yeasts were isolated from the digestive tract of basidiome-feeding beetles and lepidopteran larvae. All of the yeasts reproduced only asexually by arthroconidia and some by endo- or blastoconidia as well. Based on the comparisons of sequences in ribosomal RNA genes and other taxonomic characteristics, the yeasts were identified as three unknown Geotrichum species. The three new species are described as Geotrichum carabidarum (NRRL Y-27727^T), G. histeridarum (NRRL Y-27729^T), and G. cucujoidarum (NRRL Y-27731^T). Phylogenetic analyses from ribosomal DNA sequences showed that members of the genus Geotrichum and related arthroconidial yeast taxa were divided into two major clades: (1) Dipodascus and Galactomyces with Geotrichum anamorphs including all the new species; and (2) Magnusiomyces with Saprochaete anamorphs. G. cucujoidarum formed a subclade with G. fermentans and Geotrichum sp. Y-5419, while the two closely related species, G. carabidarum and G. histeridarum, represent a new basal subclade in the clade of Geotrichum and its teleomorphs.     

Phylogeny of the aptychi-possessing Neoammonoidea (Aptychophora nov., Cephalopoda)

The different forms of the aptychi (opercula, homologous with lower jaws) of the Ammonoidea are used for the first time in a phylogenetic analysis of part of the classic Ammonoidea phylogeny. The results indicate that the aptychi-possessing ammonoids form a monophylum for which we propose the informal name Aptychophora nov. Among the Jurassic ammonoids, it is possible to recognize several monophyletic groups. In part, our results support existing superfamilies (e.g. Hildocerataceae, Haplocerataceae) by new synapomorphies. However, the Perisphinctaceae can now be much more clearly differentiated than in the previously established phylogenetic tree. The Upper Cretaceous ammonoid superfamilies cannot be derived from the Haplocerataceae, but are descendants of a 'primitive' perisphinctacean possessing a praestriaptychus. Nor can they be derived from the 'higher' perisphinctaceans (family Perisphinctidae) because that clade is characterized by granulaptychi. The consequence of these results is that the quadrilobate primary suture of the 'Ancyloceratina' must have evolved more than once by reduction from an ancestral quinquelobate primary suture. The Ancyloceratidae have praestraptychi or aptychi types which can be derived from praestriaptychi, whereas the Crioceratitinae have longitudinally striated anaptychi.     

Fibrophrys columna gen. nov., sp. nov: A member of the family Amphifilidae

A novel Diplophrys-like organism, Fibrophrys columna, was isolated from Hiuchigaike Pond in Japan. F. columna showed a nearly orbicular or broadly elliptical cell shape and has fine filamentous, branching ectoplasmic elements emanating from both polar ends of the cell. Cells also contain orange, amber, or colorless lipid bodies. Although its whole cell morphology resembles that of the genus Diplophrys, Fibrophrys is clearly distinct from Diplophrys on the basis of 18S rDNA sequences. Molecular phylogenetic analysis showed a close relationship of F. columna with Amphifila marina, and its sequence is similar to many environmental stramenopile sequences. The cells of F. columna measured 5.0–8.3 × 5.6–10.3 μm and sometimes possessed hernia-like prongs instead of filamentous ectoplasmic elements. An axis-like electron-dense body was observed in the mitochondria. We also studied the ultrastructure of another Fibrophrys strain, Fibrophrys sp. E-1, which is different from the type strain of F. columna. A ladder-like pattern was recognized in the outer part of unidentified cytoplasmic membranes connected with the mitochondria. The unidentified cytoplasmic membranes were connected to the nuclear, lipid body, and mitochondrial outer membranes. We propose a new genus, Fibrophrys, and a new species, F. columna, based on these ultrastructural and molecular features.