How soil granulometry, temperature, and water predict genetic differentiation in Namibian spiders (Ariadna: Segestriidae) and explain their behavior

COIBar-RFLP Molecular Strategy Discriminates Species and Unveils Commercial Frauds in Fishery Products

The DNA analysis is the best approach to authenticate species in seafood products and to unveil frauds based on species substitution. In this study, a molecular strategy coupling Cytochrome Oxidase I (COI) DNA barcoding with the consolidated methodology of Restriction Fragment Length Polymorphisms (RFLPs), named COIBar-RFLP, was applied for searching pattern of restriction enzyme digestion, useful to discriminate seven different fish species (juveniles of Engraulis encrasicolus and Sardina pilchardus sold in Italy as “bianchetto” and Aphia minuta sold as “rossetto”; icefish Neosalanx tangkahkeii; European perch, Perca fluviatilis and the Nile Perch, Lates niloticus; striped catfish, Pangasianodon hypophthalmus). A total of 30 fresh and frozen samples were processed for DNA barcoding, analyzed against a barcode library of COI sequences retrieved from GenBank, and validated for COIBar–RFLP analysis. Cases of misdescription were detected: 3 samples labeled as “bianchetto” were substituted by N. tangkahkeii (2 samples) and A. minuta (1 sample); 3 samples labeled as “persico reale” (P. fluviatilis) were substituted by L. niloticus and P. hypophthalmus. All species were simultaneously discriminated through the restriction pattern obtained with MspI enzyme. The results highlighted that the COIBar-RFLP could be an effective tool to authenticate fish in seafood products by responding to the emerging interest in molecular identification technologies.

DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico

Mislabeling of seafood is a global phenomenon that can misrepresent the status and level of consumption of wild fish stocks while concealing the use of many other wild species or those originating from aquaculture and sold as substitutes. We conducted a DNA barcoding study in three cities within Mexico (Mazatlan, Mexico City and Cancun) and sequenced the COI gene in 376 fish samples sold as 48 distinct commercial names at fish markets, grocery stores, and restaurants. Our goal was to identify the main species sold, their mislabeling rates and the species most used as substitutes. Overall, the study-wide mislabeling rate was 30.8% (95% CI 26.4–35.6). Half of the samples collected belonged to five species traded globally (yellowfin tuna, Atlantic salmon, mahi, swai, and tilapia), most of them with important aquaculture or ranching production levels. These species were commonly used as substitutes for other species and showed low mislabeling rates themselves (≤ 11%, except mahi mahi with 39% mislabeling). The other half of the samples revealed nearly 100 species targeted by small-scale fishers in Mexico and sold under 42 distinct commercial names. Popular local commercial names (dorado, marlin, mero, robalo, mojarra, huachinango, pargo, sierra) showed the highest mislabeling rates (36.3% to 94.4%) and served to sell many of the 53 species identified as substitutes in our study. We discuss the observed patterns in relation to landing and import data showing differences in availability of commercial species and the links to explain observed mislabeling rates and the use of a species as a substitute for other species. We also outline some of the implications of establishing a labeling and traceability standard as an alternative to improve transparency in the trade of seafood products in Mexico.

Geographic Pattern of Sushi Product Misdescription in Italy-A Crosstalk between Citizen Science and DNA Barcoding

The food safety of sushi and the health of consumers are currently of high concern for food safety agencies across the world due to the globally widespread consumption of these products. The microbiological and toxicological risks derived from the consumption of raw fish and seafood have been highlighted worldwide, while the practice of species substitution in sushi products has attracted the interest of researchers more than food safety agencies. In this study, samples of sushi were processed for species authentication using the Cytochrome Oxidase I (COI) gene as a DNA barcode. The approach of Citizen Science was used to obtain the sushi samples by involving people from eighteen different Italian cities (Northern, Central and Southern Italy). The results indicate that a considerable rate of species substitution exists with a percentage of misdescription ranging from 31.8% in Northern Italy to 40% in Central Italy. The species most affected by replacement was Thunnus thynnus followed by the flying fish roe substituted by eggs of Mallotus villosus. These results indicate that a standardization of fish market names should be realized at the international level and that the indication of the scientific names of species should be mandatory for all products of the seafood supply chain.

Novel Amino Acid Assembly in the Silk Tubes of Arid-Adapted Segestriid Spiders

We investigated in different sites inside or outside the Namib Desert the amino acids composition of the protein material forming the tube silk of Ariadna spiders. These spiders belong to the primitive Segestriidae family and spend their life inside vertical silk burrows dug within the sandy and gravelly soil of arid areas. The silks, previously purified by solubilization in hexafluoroisopropanol, were subjected to partial or total acid hydrolysis. Partial hydrolyzed samples, analyzed by mass spectrometry (matrix assisted laser desorption/ionization and electrospray), led to relevant information on the amino acid sequences in the proteins. The free amino acids formed by complete hydrolysis were derivatized with the Marfey's reagent and characterized by electrospray mass spectrometry. The reconstruction of the amino acids highlights a homogeneous plan in the chemical structure of all the analyzed silks. Eight amino acids constituting the primary structure of the proteins were identified. Alanine and glycine are the most abundant ones, with a prevalence of alanine, constituting together at least 61% of the chemical composition of the protein material, differently from what occurs in known spidroins. High percentages of proline, serine and threonine and low percentages of leucine complete the peculiarity of these proteins. The purified silks were also characterized by Fourier-transform Infrared Spectroscopy and their thermal properties were investigated by differential scanning calorimetry. The comparison of the silk tubes among the various Namibian populations, carried out through a multivariate statistical analysis, shows significant differences in their amino acid assembly possibly due to habitat features.

Swordfish or Shark Slice? A Rapid Response by COIBar-RFLP

Market transparency is in strong demand by consumers, and the authentication of species is an important step for seafood traceability. In this study, a simple molecular strategy, COIBar–RFLP (cytochrome oxidase I barcode–restriction fragment length polymorphism), is proposed to unveil commercial fraud based on the practice of species substitution in the swordfish trade. In particular, COI barcoding allowed the identification of the species Prionace glauca, Mustelus mustelus, and Oxynotus centrina in slices labeled as Xiphias gladius. Furthermore, the enzymatic digestion of COI amplicons using the MboI restriction endonuclease allowed the simultaneous discrimination of the four species. Interestingly, an intraspecific differential MboI pattern was obtained for the swordfish samples. This pattern was useful to differentiate the two different clades revealed in this species by phylogenetic analyses using several molecular markers. These results indicate the need to strengthen regulations and define molecular tools for combating the occurrence of fraud along the seafood supply chain and show that COIBar–RFLP could become a standardized molecular tool to assess seafood authenticity.

Microbiomics of Namib Desert habitats

The Namib Desert is one of the world's only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.

From Fish Eggs to Fish Name: Caviar Species Discrimination by COIBar-RFLP, an Efficient Molecular Approach to Detect Fraud in the Caviar Trade

The demand for caviar is growing as is its price on the market. Due to the decline of true caviar production from sturgeons, eggs from other fish species and other animals have been used as substitutes for caviar. The labels on these products should indicate the species from which the eggs were derived, but the label can be misleading in some cases. In this context, species identification using DNA analysis is crucial for traceability and authentication of caviar products. In this work, we applied the COIBar-RFLP procedure to obtain species-specific endonuclease restriction patterns useful to discriminate “caviar” species. The tested caviar products were identified as originating from eight species: Acipenser transmontanus, A. gueldenstaedtii, A. stellatus, A. baerii, Mallotus villosus, Huso huso, Cyclopterus lumpus and Eumicrotremus orbis. The results demonstrated that 14% of the caviar products examined have a label that does not indicate the species from which the eggs were originated. The MboI restriction enzyme produced specific profiles discriminating the eight species, confirming that the COIBar-RFLP is a useful approach for routine screening of seafood products due to its ease and rapid execution, as the results of screening can be obtained within 7 h, by-passing the need for sequencing.