Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths

The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.     

Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

Bifidobacteria represent one of the dominant microbial groups that are present in the gut of various animals, being particularly prevalent during the suckling stage of life of humans and other mammals. However, the overall genome structure of this group of microorganisms remains largely unexplored. Here, we sequenced the genomes of 42 representative (sub)species across the Bifidobacterium genus and used this information to explore the overall genetic picture of this bacterial group. Furthermore, the genomic data described here were used to reconstruct the evolutionary development of the Bifidobacterium genus. This reconstruction suggests that its evolution was substantially influenced by genetic adaptations to obtain access to glycans, thereby representing a common and potent evolutionary force in shaping bifidobacterial genomes.     

A CRISPR design for next-generation antimicrobials

Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance.     

Antihypertensive and endothelium-dependent vasodilator effects of aqueous extract of Cistus ladaniferus

Cistus ladaniferus L. (Cistaceae) is a medicinal plant originated from the Mediterranean region which exerts different pharmacological effects. In the present study, our goal was to examine whether the plant possessed antihypertensive properties. Aqueous extract of Cistus leaves (AEC, 500 mg/kg/day) reduced systemic blood pressure (SBP) in two animal models of hypertension, the l-NAME and renovascular two kidney-one clip (2K-1C) hypertensive rats. In the former, AEC prevented the increase in SBP when co-administered with l-NAME during four weeks (164 ± 3 mm Hg in l-NAME vs. 146 ± 1 mm Hg in l-NAME + AEC, p < 0.001). In the latter, AEC reversed the increase in SBP when administered during four weeks after installation of the hypertension (146 ± 5 mm Hg with AEC vs. 179 ± 6 mm Hg without, p < 0.05). AEC treatment also reversed the endothelial dysfunction observed in both animal models of hypertension. A direct effect on cardiac and vascular tissue was also tested by examining the contractile effects of AEC in rat isolated aortic rings and Langendorff perfused hearts. AEC (10 mg/L) had no effect on left ventricular developed pressure and heart rate in isolated perfused heart. However, AEC produced a strong relaxation of pre-contracted rat aortic rings (80 ± 2% relaxation, n = 25). When the rings were denuded from endothelium or were incubated with 1 mM Nω-nitro-l-arginine (l-NNA), the relaxant effect of AEC was lost. We conclude that C. ladaniferus possesses antihypertensive properties which are mainly due to an endothelium-dependent vasodilatory action.     

Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms,Insertions, and Deletions

Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.Probiotics are currently defined as live microorganisms which, when administered in adequate amounts, confer a health benefit on the host (12). Many of the organisms studied for their probiotic potential are members of lactic acid bacteria and the genus Bifidobacterium, which has resulted in their inclusion in a large variety of dietary supplements and food products. Relative to most bifidobacterial species of human origin, Bifidobacterium animalis subsp. lactis is less sensitive to stressful conditions (bile, acid, and oxygen) which might be encountered in the mammalian gastrointestinal tract or in fermented or acidified dairy products (7, 26, 28, 31, 37). B. animalis subsp. lactis is widely added to commercial products because it is better able to withstand the adverse conditions of starter culture and product manufacture and to maintain viability and stability during product shelf-life (30). Therefore, strains of B. animalis, specifically B. animalis subsp. lactis, have been found in the majority of probiotic-supplemented dairy products surveyed in North America (the United States and Canada) and Europe (Great Britain, France, Italy, and Germany) (6, 13-15, 21, 22, 28, 29, 32, 49).When selecting a probiotic microorganism to add to supplements or foods, the strain must be identified at the genus, species, and strain levels (40). Proper characterization of a strain is important for safety and quality assurance, for identifying and differentiating putative probiotic strains, and for understanding the interactions among members of gut microbiota. In addition, proper characterization is important to maintain consumer confidence. Product labels often list invalid names of organisms or misidentify the species the product contains, leading to consumer confusion (6, 16, 20, 28, 29, 35, 38, 49). In the case of Bifidobacterium, most dairy products sold in the United States do not identify species, and many only refer to the invalid name “Bifid” or “Bifidus.” At the very least, added microorganisms should be accurately identified to the species level on product labels.According to the FAO/WHO guidelines for probiotic use, specific health benefits observed in research using a specific strain cannot be extrapolated to other, closely related strains (12). Although most clinical studies of probiotic strains compare strains of different genera or different species, few studies have assessed the actual variability of expected health benefits within species or subspecies. However, it is reasonable to consider that health effects, like the phenotypic traits exhibited by strains within a species, are strain specific. Therefore, reliable techniques for the identification of probiotic organisms at the strain level are required.Characterization to the strain level has several important potential applications. Understanding the complex interactions among microorganisms in the intestinal ecosystem requires methods of differentiating a strain of interest from other strains of the same species contained in the autochthonous microbiota. Strain differentiation techniques also aid in assessing survival of a probiotic organism through the gastrointestinal system, which is particularly important for clinical trials and regulatory purposes (17). The ability to uniquely identify a strain also lends credibility to statements made about the potential health benefits of consuming a particular product containing a strain with demonstrated probiotic effects and supports the licensing or intellectual property rights of the manufacturer.The high degree of genome conservation observed between strains of B. animalis subsp. lactis in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies (2, 25; also HN019 GenBank project 28807). As an example, comparison of the complete genome sequences of two B. animalis subsp. lactis strains, DSMZ 10140 (the type strain) and Bl-04 (a commercial strain, also known as RB 4825) (2), identified 47 single-nucleotide polymorphisms (SNPs) in nonrepetitive elements, as well as 443 bp distributed among four INDEL sites: a 121-bp tRNA-encoding sequence, a 54-bp region within the long-chain fatty acid-coenzyme A ligase gene, a 214-bp region within the CRISPR (clustered regularly interspaced short palindromic repeats) locus, and a 54-bp intergenic sequence. Overall, this 99.975% genome identity explains the inability to differentiate these strains by techniques such as the sequencing of housekeeping genes, multilocus sequence typing, and pulsed-field gel electrophoresis (PFGE) (3, 9, 23, 39, 44-46, 50).The strain specificity of reported health benefits of probiotics and the frequent use of B. animalis subsp. lactis as a probiotic in food products and supplements demands techniques with greater discriminatory power to identify and differentiate among strains within this highly homogeneous group. Unfortunately, strain level differentiation of B. animalis subsp. lactis presents several challenges. Although Ventura and Zink were able to differentiate strains of B. animalis subsp. lactis by sequencing the 16S-23S internal transcribed sequence (ITS) region (47), analysis of the four ITS operons between DSMZ 10140 and Bl-04 indicated complete identity (2). However, SNPs and INDELs do have potential for strain differentiation. According to Achtman, focusing on polymorphic SNPs is a desirable approach for the typing of monomorphic species (1). Therefore, the objective of the present study was to exploit the previously identified SNP and INDEL sites to develop a technique capable of differentiating among a collection of B. animalis subsp. lactis strains obtained from culture collections and commercial starter culture companies.     

Synthesis, crystal structure and characterizations of iron(III) and copper(II) complexes with the hydrazone ligand obtained from 2-formyl-pyridine and Girard’s T reagent

The condensation of 2-formyl-pyridine with Girard’s T reagent yields a new hydrazone in the form of an ammonium quaternary salt: [H(2-PyGT)]Cl. This tridentate ligand is readily soluble in water and reacts with iron(III) or copper(II) chlorides to give [Fe(2-PyGT)Cl₃] (1) or [Cu(2-PyGT)Cl₂]·(H₂O) (2) complexes, respectively. Single-crystal X-ray studies in 1 and 2 reveal that the coordination reaction gives rise to the deprotonation of the organic ligand that is coordinated using its NNO donor atoms in the form of a zwitterion species. The coordination spheres around the transition metal ions in complexes 1 and 2 are quite different. In 1, the iron site adopts a distorted octahedral coordination sphere, while the Cu(II) ions in 2 show a distorted tetragonal-pyramid geometry. As expected, the magnetic properties of these compounds reveal only weak antiferromagnetic interaction between spin carriers.     

AB INITIO Simulations of Desorption and Reactivity of Glycine at a Water-Pyrite Interface at “Iron-Sulfur World” Prebiotic Conditions

Glycine at the interface of a pyrite surface (001) FeS₂, and bulk water at high pressure and temperature conditions relevant to the “iron-sulfur world” scenario of the origin of life is investigated by theoretical means. Car-Parrinello molecular dynamics is used in order to study the desorption process of the zwitterionic form of this amino acid using two different adsorption modes, where either only one or both oxygens of the carboxylate group are anchored to surface iron atoms. It is found that the formation of stabilizing hydrogen bonds plays a key role in the detachment process, leading to longer retention times for the bidentate adsorption mode. In addition, the chemical reactivity of this heterogeneous system is probed by calculating the Fukui functions as site-specific reactivity indices. The most prominent targets for both nucleophilic and electrophilic reactions to occur are surface atoms, whereas the reactivity of glycine is only slightly affected upon anchoring.     

Effect of microbial pathogens on the diversity of aquatic populations, notably in Europe

The expansion of aquaculture and the demand for ornamental fish have resulted in the large-scale movements of aquatic animals and their pathogens. Here we review the most important non-native fish and shellfish pathogens in European waters and their global impacts on wild fish host populations. The role of theoretical models in the study of the impact of microbial pathogens is discussed, including its integration into risk assessments.