Mitochondrial, morphological and environmental data partially support current subspecies designation in Amazilia yucatanensis hummingbirds

Historical geological events and Pleistocene climatic fluctuations have played important roles in shaping distribution and population differentiation across taxa. The buff-bellied hummingbird (Amazilia yucatanensis) is widely distributed along the Gulf of Mexico slope and the Yucatan Peninsula. Here, we obtained measurements and sequenced two mitochondrial DNA fragments from currently recognized subspecies: Amazilia yucatanensis yucatanensis (YUC), Amazilia yucatanensis cerviniventris (CER) and Amazilia yucatanensis chalconota (CHA). Additionally, we tested for their genetic and morphological differentiation, demographic expansion, palaeoclimatic distribution and niche overlap. Our results reveal genetic differentiation between two groups of populations: (1) from the Yucatan Peninsula to Veracruz (YUC+CER); and (2) from Veracruz to Tamaulipas (CHA). Neutrality tests and Bayesian skyline plots suggest past demographic expansion without changes in the effective population size over time. The potential distribution was fragmented at the Trans-Mexican Volcanic Belt and expanded northwards during the Last Glacial Maximum and Mid-Holocene to current conditions. Niche overlap was higher between YUC and CER. The environmental space occupied by subspecies was more similar to each other than expected by chance but significantly non-equivalent. Our results provide new insight on the distribution of this widespread hummingbird species and suggest that fragmentation during glaciations and differences in habitat have played a role in the recent diversification.

Phylogeography supports lineage divergence for an endemic rattlesnake (Crotalus ravus) of the Neotropical montane forest in the Trans-Mexican Volcanic Belt

The formation of the Trans-Mexican Volcanic Belt (TMVB) and Pleistocene climatic fluctuations have been shown to influence the diversification of lineages and species distributed throughout central Mexico. In some taxa, however, evidence of lineage diversification is not easily recognized, as often is the case in reptiles. Here we present a phylogeographic study on a Mexican endemic rattlesnake species (Crotalus ravus), with the aim of understanding how distinct lineages are distributed across the TMVB. Genetic (mtDNA) and genomic (ddRADseq) data were generated from samples across the species’ range to evaluate phylogeographic structure, estimate phylogenetic relationships and divergence times, and perform environmental niche modeling (ENM). Both datasets recover strong phylogeographic structuring of two distinct lineages on an east-west axis, with an estimated Pleistocene divergence (~1.47 Myr). The ENM suggest that the distribution of the two lineages experienced expansion and reduction events throughout recent evolutionary time. We attribute the diversification of C. ravus lineages to geological events associated with the formation of the TMVB, as well as Quaternary climate changes, both of which have been previously recognized in co-distributed taxa in the TMVB. This work emphasizes the existence of cryptic diversification processes in a morphologically conserved species distributed in a region of complex climatic and orogenic heterogeneity.

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Background

The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs).

Objective

This study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs.

Methods

30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed.

Results

148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes.

Conclusion

The COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.

Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico

The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Shelf-life of traditionally-seasoned

Few studies have been carried out to determine the shelf-life of the Aloreña de Málaga table olive packaging from a physicochemical, microbiological and sensorial point of view. This study showed that under the current packaging conditions, commercial products were free from Enterobacteriaceae, the initial yeast population was progressively inhibited, and only lactic acid bacteria grew during shelf-life. Among the physicochemical characteristics, pH decreased, lactic acid was formed while citric acid and mannitol were consumed. These changes resulted in gradual olive texture degradation and green color fading during packaging. A multivariate analysis showed that the packaged olives with storage time between 6 and 42 days enjoyed the highest acceptance; while after the 74th day, they were progressively losing acceptability, which was mainly evident at the 131st day of packaging (willingness-to-buy attribute was reduced to 50%). A complete microbiological stabilization would require the use of alternative preservatives since thermal treatment is not convenient for this type of olive speciality.

Assessment of the bacterial community in directly brined Aloreña de Málaga table olive fermentations by metagenetic analysis

This study uses an "omics" approach to evaluate the bacterial biodiversity changes during fermentation process of natural green cracked Aloreña de Málaga table olives, from raw material to fermented fruit. For this purpose, two industries separated by almost 20km in Guadalhorce Valley (Málaga, Spain) were analysed for obtaining both brines and fruit samples at different moments of fermentation (0, 7, 30 and 120days). Physicochemical and microbial counts during fermentation showed the typical evolution of this type of processes, apparently dominated by yeasts. However, high-throughput barcoded pyrosequencing analysis of V2-V3 hypervariable region of the bacterial 16S rRNA gene showed at 97% identity the presence of 131 bacterial genera included in 357 operational taxonomic units, not detected by the conventional approach. The bacterial biodiversity was clearly higher in the olives at the moment of reception in the industry and during the first days of fermentation, while decreased considerably as elapse the fermentation process. The presence of Enterobacteriaceae and Lactobacillaceae species was scarce during the four months of study. On the contrary, the most important genus at the end of fermentation was Celerinatantimonas in both brine (95.3% of frequency) and fruit (89.4%) samples, while the presence of well-known spoilage microorganisms (Pseudomonas and Propionibacterium) and halophilic bacteria (Modestobacter, Rhodovibrio, Salinibacter) was also common during the course of fermentation. Among the most important bacterial pathogens related to food, only Staphylococcus genus was found at low frequencies (<0.02% of total sequences). Results show the need of this type of studies to enhance our knowledge of the microbiology of table olive fermentations. It is also necessary to determine the role played by these species not previously detected in table olives on the quality and safety of this fermented vegetable.

Fortification of table olive packing with the potential probiotic bacteria Lactobacillus pentosus TOMC-LAB2

Dairy products are currently the main carriers of probiotic microorganisms to the human body. However, the development of new matrices for probiotic delivery is convenient for intolerant to milk (or its derivatives) and those requiring low-cholesterol diet consumers. The present work focused on the fortification of previously fermented green Spanish style olives with the autochthonous putative probiotic bacteria Lactobacillus pentosus TOMC-LAB2. The fortification was carried out by inoculating the bacteria into the packing brines using Manzanilla fruits from three different processes: (i) spontaneously fermented (F1), (ii) fermented using L. pentosus TOMC-LAB2 as starter (F2), and (iii) spontaneously fermented and then thermally treated (F3). Data showed that all inoculated treatments had higher population levels (5.49, 4.41, and 6.77 log₁₀ cfu/cm²) than their respective controls (1.66, 4.33, and 0.0 log₁₀ cfu/cm², for F1, F2, and F3 treatments, respectively). The presence of L. pentosus TOMC-LAB2 on olive surface was confirmed by rep-PCR, with a recovery frequency at the end of the shelf life (200 days) of 52.6, 57.9, and 100.0% for F1, F2, and F3 treatments, respectively. Thus, results obtained in this work show the ability of this microorganism to survive under packing conditions for long period of times as well as to colonize the olive surface which is the food finally ingested by consumers. This opens the possibility for the development of a new and simply probiotic fortified olive product.

Selection of yeasts with multifunctional features for application as starters in natural black table olive processing

Yeasts are unicellular eukaryotic microorganisms with a great importance in the elaboration on many foods and beverages. In the last years, researches have focused their attention to determine the favourable effects that these microorganisms could provide to table olive processing. In this context, the present study assesses, at laboratory scale, the potential technological (resistance to salt, lipase, esterase and β-glucosidase activities) and probiotic (phytase activity, survival to gastric and pancreatic digestions) features of 12 yeast strains originally isolated from Greek natural black table olive fermentations. The multivariate classification analysis carried out with all information obtained (a total of 336 quantitative input data), revealed that the most promising strains (clearly discriminated from the rest of isolates) were Pichia guilliermondii Y16 (which showed overall the highest resistance to salt and simulated digestions) and Wickerhamomyces anomalus Y18 (with the overall highest technological enzymatic activities), while the rest of strains were grouped together in two clearly differentiated clusters. Thus, this work opens the possibility for the evaluation of these two selected yeasts as multifunctional starters, alone or in combination with lactic acid bacteria, in real table olive fermentations.

Microbial stability and quality of seasoned cracked green Aloreña table olives packed in diverse chloride salt mixtures

This work was conducted to determine the effect of the partial replacement of NaCl by KCl and CaCl2 (expressed as percentages, wt/vol) on the microbial stability and physicochemical characteristics of seasoned cracked olives using a simplex centroid mixture design. Neither Enterobacteriaceae nor lactic acid bacteria were found during the 50 days that olive packages were monitored. Therefore, microbial instability was considered due to the growth of yeasts, which were the only detected microorganisms; Saccharomyces cerevisiae and Pichia membranifaciens were the most relevant species. Yeasts decreased during the first 21 to 30 days after packing, but their populations rose to 3.5 log CFU/ml by the end of the storage period, clearly causing product deterioration. The partial substitution of NaCl with the other chloride salts slightly altered the phase of microbial inhibition and regrowth. Most of the quality characteristics were not affected by the use of the alternative salt mixtures, but the pH values and Cl(-) concentrations in brine decreased as the CaCl2 concentration increased. Hence, seasoned cracked table olives can be produced using a lower proportion of NaCl without causing significant changes in the shelf life and product quality, although further detailed studies are necessary to guarantee the stability of products packed with specific salt mixtures.

Evaluating the individual effects of temperature and salt on table olive related microorganisms

Statistical modelling techniques were used in the present study to assess the individual effects of temperature and NaCl concentration on the growth of 10 lactic acid bacteria and 6 yeast strains mostly isolated from different forms of table olive processing and belonging to the species Lactobacillus pentosus, Lactobacillus plantarum, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Candida boidinii. The mathematical models obtained in synthetic laboratory media show that yeasts, except for C. boidinii, were more resistant to a high salt concentration than lactic acid bacteria, with an MIC value ranging from 163.5 (S. cerevisiae) to 166.9 g/L (W. anomalus); while for L. pentosus and L. plantarum this parameter ranged from 110.6 to 117.6 g/L, respectively. With regards to temperature, lactic acid bacteria showed a slight trend towards supporting higher temperature values than yeasts, with the exception of S. cerevisiae. The maximum temperatures for growth of L. pentosus and L. plantarum were 41.9 and 43.0 °C, respectively; while for W. anomalus and C. boidinii they were 38.2 and 36.5 °C. The optimum temperatures for growth were also higher for L. pentosus and L. plantarum (35.5 and 32.9 °C), compared to W. anomalus and C. boidinii (29.3 and 26.9 °C, respectively). Additional experiments carried out in natural olive brines confirmed previous results, showing that high NaCl concentrations clearly favoured yeast growth and that at high temperatures LAB slightly overcame yeasts. Results obtained in this paper could be useful for industry for a better control of both table olive fermentation and packaging.

Yeasts in table olive processing: desirable or spoilage microorganisms?

Yeasts are unicellular eukaryotic microorganisms isolated from many foods, and are commonly found in table olive processing where they can play a double role. On one hand, these microorganisms can produce spoilage of fruits due to the production of bad odours and flavours, the accumulation of CO(2) leading to swollen containers, the clouding of brines, the softening of fruits and the degradation of lactic acid, which is especially harmful during table olive storage and packaging. But on the other hand, fortunately, yeasts also possess desirable biochemical activities (lipase, esterase, β-glucosidase, catalase, production of killer factors, etc.) with important technological applications in this fermented vegetable. Recently, the probiotic potential of olive yeasts has begun to be evaluated because many species are able to resist the passage through the gastrointestinal tract and show beneficial effects on the host. In this way, yeasts may improve consumers' health by decreasing cholesterol levels, inhibiting pathogens, degrading non assimilated compounds, producing antioxidants and vitamins, adhering to intestinal cells or by maintaining epithelial barrier integrity. Many yeast species, usually also found in table olive processing, such as Wicherhamomyces anomalus, Saccharomyces cerevisiae, Pichia membranifaciens and Kluyveromyces lactis, have been reported to exhibit some of these properties. Thus, the selection of the most appropriate strains to be used as starters, alone or in combination with lactic acid bacteria, is a promising research line to develop in a near future which might improve the added value of the commercialized product.

Evaluating the effects of zinc chloride as a preservative in cracked table olive packing

This survey studies the influence of different zinc chloride concentrations (0.050, 0.075, and 0.100%, wt/vol) on the shelf life of "Aceituna Aloreña de Málaga" table olives. The Enterobacteriaceae population significantly (P ≤ 0.05) decreased in treatments containing 0.050 and 0.100% ZnCl(2), and those with 0.075% ZnCl(2) had also lower average counts than those observed under the usual packaging conditions (0.12% potassium sorbate). Lactic acid bacteria increased for treatments with 0.050 and 0.075% ZnCl(2), but in the presence of 0.100% they practically disappeared at the end of the shelf life period (∼3 months). With respect to yeasts, populations of these microorganisms significantly decreased with the first two concentrations (0.050 and 0.075%) but showed a slight increase in the presence of 0.100% of ZnCl(2), although remaining markedly below populations observed with potassium sorbate packing. The use of this chloride salt also led to products with higher concentrations of sugars in brine because of its selective microbial inhibition. Finally, olives treated with 0.075% ZnCl(2) showed an improved sensory profile.

Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.

Exploring the yeast biodiversity of green table olive industrial fermentations for technological applications

In recent years, there has been an increasing interest in identifying and characterizing the yeast populations associated with diverse types of table olive elaborations because of the many desirable technological properties of these microorganisms. In this work, a total of 199 yeast isolates were directly obtained from industrial green table olive fermentations and genetically identified by means of a RFLP analysis of the 5.8S-ITS region and sequencing of the D1/D2 domains of the 26S rDNA gene. Candida diddensiae, Saccharomyces cerevisiae and Pichia membranifaciens were the most abundant yeast species isolated from directly brined Aloreña olives, while for Gordal and Manzanilla cultivars they were Candida tropicalis, Pichia galeiformis and Wickerhamomyces anomalus. In the case of Gordal and Manzanilla green olives processed according to the Spanish style, the predominant yeasts were Debaryomyces etchellsii, C. tropicalis, P. galeiformis and Kluyveromyces lactis. Biochemical activities of technological interest were then qualitatively determined for isolates belonging to all yeast species. This preliminary screening identified two isolates of W. anomalus with interesting properties, such as a strong β-glucosidase and esterase activity, and a moderate catalase and lipolytic activity, which were also confirmed by quantitative assays. The results obtained in this survey show the potential use that some yeast species could have as starters, alone or in combination with lactic acid bacteria, during olive processing.

Effect of storage process on the sugars, polyphenols, color and microbiological changes in cracked Manzanilla-Aloreña table olives

The green cracked "seasoned" Manzanilla-Aloreña table olive is a specialty with a high demand when prepared from fresh fruits; however, when stored fruits are used, the product loses its green color, presents a brownish tone, and loses demand. Different alternative storage systems for preventing such changes and preserving the freshness of the fruits were studied, and their effects on sugar, polyphenol, color, and microbiological changes were analyzed. The application of two washing waters in the presence of different compounds before brining markedly decreased the sugar and polyphenol contents in the flesh, without negatively influencing the color; it also caused the inhibition of yeasts and lactic acid bacteria (except in treatments using sodium metabisulfite and saturated carbon dioxide (CO(2)) in the storage olive brines. Salicylic acid inhibited microbial growth during washings and storage. The best long-term color was achieved in the presence of sodium metabisulfite. A combination of two washing waters (containing 5% sodium chloride (NaCl) and 0.1% sodium metabisulfite or saturated CO(2)), followed by immersion of the fruits in 15% NaCl brine with 0.1% sodium metabisulfite or brine under saturated CO(2) added, led to the best storage conditions.