Genetic Diversity of Listeria monocytogenes Isolated From Three Commercial Tree Fruit Packinghouses and Evidence of Persistent and Transient Contamination

Whole genome analysis was performed on 501 isolates obtained from a previous survey which recovered 139 positive environmental sponge samples (i.e., up to 4 isolates per sample) from a total of 719 samples collected at 40 standardized sites in 3 commercial apple packinghouse facilities (i.e., P1, P2, and P3) over 3 successive seasons in a single production year. After excluding duplicated isolates, the data from 156 isolates revealed the clonal diversity of L. monocytogenes and allowed the detection of transient contamination, persistent contamination, and cross-area transmission events. Facility P2 with the poorest sanitary conditions had the least diversity (Shannon’s index of 0.38). P2 contained a Clonal Complex (CC) 554, serogroup IVb-v1 strain that persisted throughout the year and spread across the entire facility, a singleton Sequence Type (ST) 1003, lineage III strain that persisted through two seasons and spread across two areas of the facility, and 3 other clones from transient contaminations. P1 and P3, facilities with better sanitary conditions, had much higher diversity (i.e., 15 clones with a Shannon’s index of 2.49 and 10 clones with a Shannon’s index of 2.10, respectively) that were the result of transient contamination. Facilities P1 and P3 had the highest incidence (43.1%) of lineage III isolates, followed by lineage I (31.3%) and lineage II (25.5%) isolates. Only 1 isolate in the three facilities contained a premature stop codon in virulence gene inlA. Fourteen samples yielded 2–3 clones per sample, demonstrating the importance of choosing appropriate methodologies and selecting a sufficient number of isolates per sample for studying L. monocytogenes diversity. Only 1 isolate, belonging to CC5 and from facility P3, contained a known plasmid, and this was also the only isolate containing benzalkonium chloride tolerance genes. The persistent CC554 strain did not exhibit stronger sanitizer resistance than other isolates and did not contain any confirmed molecular determinants of L. monocytogenes stress resistance that were differentially present in other isolates, such as genes involved in sanitizer tolerance, heavy metal resistance, biofilm-forming, stress survival islet 1 (SSI-1), stress survival islet 2 (SSI-2) or Listeria genomic island (LGI2).

Characterization of Zymoseptoria tritici populations in Belarus by morphologic and cultural features

Septoria leaf blotch caused by Zymoseptoria tritici is one of the most harmful diseases in Belarus. Isolates of the pathogen were obtained from northern, central and southern populations: in 2018–2019, whichvaried significantly among in the structure of colonies. The rate of fungal isolates forming yeast-like colonies decreased from 55.0 % in the North of Belarus to 6.7 % in the South, whereas incidence of filamentous isolates increased from 31.3 % to 80.0 %, respectively. In the northern population, phenotypic diversity was high, while in the southern population it was the lowest (Shannon’s index was 1.53 and 1.14, respectively).

Comparative analysis of the diet of members of the families Mustelidae and Canidae

The article analyzes 151 food samples of carnivoran mammals of two families. It was found that the diet includes 49 food items in the studied species of the family Canidae and 42 items in species of the family Mustelidae, of both plant and animal origin. It was revealed that plant food is an important component of the diet of predators, since the frequency of registration of these objects is 46.4%. Most often, it is the remains of cereals and plant seeds. Rodents are the main food for both families (19% in Canidae, 21% in Mustelidae). A seasonal change in diet for both families was noted. Members of the family Mustelidae consume plants more often in summer and winter, while in in spring and autumn mammals prevail in their diet when the share of juicy fruits is the lowest. Rodents are consumed throughout the year, but their largest share was noted in spring, when this family is characterized by the greatest variety of food (Shannon's index is 2.0). For members of the family Canidae, the most important component of the diet in winter is dry fruits. The number of rodents in their diet also increases in spring. The summer period is characterized by the consumption of invertebrates and the absence of animal carcasses in the diet. In autumn, the share of juicy fruits increases and during this period the diet of Canidae is the most diverse (1.9). The lowest variety of food in species of the two families was registered in summer. Competition between the studied families may increase in spring when the most important food for the representatives of both Canidae and Mustelidae is rodents. There are some sex-related trophic preferences in both families. In particular, males of the family Mustelidae consume rodents more often (68.7%), while females more often feed on plants (56.1%). As for the family Canidae, the analysis was carried out on the example of the red fox. It was found that females of this species prefer plant foods and there are no ungulates in their diet. Males consume fewer plants (41.4%) and often forage in cattle burial grounds and landfills. Accordingly, the diet of males is more diverse compared to that in females. The Shannon index is 3.3 and 2.5, respectively.

Comparison of culture-based strategies for isolating bacteria from the porcine intestine

The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious, and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of bacteria from the intestine of pigs as a model animal, and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified Ichip, as well as ethanol and Tyndallization treatment of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and seven phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon’s index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with Tyndallization yielding a lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was greatest for ethanol-treated samples (41.9%) and the Ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals. IMPORTANCE This work determined that using a combination of isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g. diffusion methods [i.e. Ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the Ichip method delivered similar diversity of bacteria to enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition to other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.

Waterbird abundance and diversity along a stretch of Ganga River, India modified by construction of a barrage

Damming and diverting river water alters the channel characteristics and natural flow regime. The change in biotic and abiotic factors results in dissimilar habitat conditions upstream and downstream of the barrage. Given the habitat dissimilarity and therefore resource availability, we hypothesized the dissimilarity in waterbird abundance and species diversity in the river habitat upstream and downstream of the barrage. The study was conducted on a 24 km stretch of Ganga River at Narora, Uttar Pradesh, India. This stretch overlaps with a Ramsar site as well as an Important Bird and Biodiversity Area (IBA). Bird sampling was done using transect count method for summer and winter season in 2017. The abundance was studied in relation to three habitat variables viz. channel depth, channel width and anthropogenic disturbances using Generalized Linear Model. A total of 140 species of birds were recorded. There was statistically significant difference in the abundance of waterbirds between upstream and downstream stretch in winter season (Mann-Whitney U, p < 0.05). During winters, migratory waterbirds especially ducks and geese occupied the deep water upstream of barrage, while the downstream was mostly occupied by terns and cormorants. Waterbird species diversity was higher in downstream during winters (Effective Number of Species=28; Shannon’s Index= 3.35) and higher in upstream during summer (Effective Number of Species=25, Shannon’s Index=2.87). Channel width, channel depth and anthropogenic disturbance influenced waterbird abundance in both the seasons (Generalized Linear Model; p < 0.05). The influence of channel depth varied with season for the upstream stretch.

Diversity in substance use behaviour among street children of Delhi under Bayesian paradigm

Background Shannon’s index is one of the measures of biodiversity, which is intended to quantify both richness and evenness of the species/individuals in the ecosystem or community. However, application of Shannon’s index in the field of substance use among the street children has not been done till date. Methods This paper is concerned with methods of estimating Shannon’s diversity index (SDI), which can be used to capture the variation in the population due to certain characteristics. Under the consideration that the probability of abundance, based on certain characteristics in the population, is a random phenomenon, we derive a Bayesian estimate in connection with Shannon’s information measure and their properties (mean and variance), by using a probability matching prior, through simulation and compared it with those of the classical estimates of Shannon. The theoretical framework has been applied to the primary survey data of substance use among the street children in Delhi, collected during 2015. The measure of diversity was estimated across different age profiles and districts. Results The results unrevealing the diversity estimate for street children corresponding to each region of Delhi, under both the classical and Bayesian paradigms. Although the estimates were close to one another, a striking difference was noted in the age profile of children. Conclusions The Bayesian methodology provided evidence for a greater likelihood of finding substance-using street children, belonging to the lower age group (7-10, maximum Bayesian entropy-3.73), followed by the middle (11-14) and upper age group (15-18). Moreover, the estimated variance under the Bayesian paradigm was lesser than that of the classical estimate. There is ample scope for further refinement in these estimates, by considering more covariates that may have a possible role in initiating substance use among street children in developing countries like India.

Evenness-richness scatter plots: a graphical, intuitive approach to alpha diversity analysis

Shannon’s diversity index is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent of both those parameters, there is theoretically an infinite number of richness / evenness value combinations translating into the same index score. By decoupling both components measured by Shannon’s index, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as PERMANOVA can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise.

DIETARY ANALYSIS OF THREE SPECIES OF THE GENUS Anolis (SAURIA: DACTYLOIDAE) IN “LOS TUXTLAS,” VERACRUZ, MEXICO

Anoles have been studied by researchers to a greater extent than any other group of lizards. Their high diversity has led them to colonize a variety of niches, making them an ideal model group for evaluating ecological hypotheses such as dietary niche overlap. This work analyzes the stomach contents of 73 individuals from three species of the genus Anolis: A. barkeri (34), A. sericeus (17), and A. tropidonotus (22) occurring in the vicinity of Los Tuxtlas, Veracruz. Analyses performed included Shannon’s index in its log form to calculate dietary diversity, the Jaccard index to estimate the dissimilarity of the species’ diets, and Schoener’s index to measure dietary overlap. The results suggest that A. barkeri (10.08) hast the most generalist diet, followed by A. sericeus (8.75) and A. tropidonotus (5.78). Schoener’s index showed a considerable amount of diet overlap between A. barkeri and A. sericeus (0.76). We conclude that the three focal species show a generalist feeding behavior in times of abundant prey, such as the rainy season in which this study was conducted. This may lead to the elusion of intra-generic competition, explaining why we did not observe dietary niche displacement between these three species of Anolis.

Genetic diversity of Piracanjuba populations in fish stocking programs in the Tietê River, Brazil

Background: Piracanjuba (Brycon orbignyanus) is a fish species highly affected by anthropogenic actions such as overfishing, water pollution, and hydroelectric developments. This species is currently considered in danger of extinction. Objective: To analyze the genetic diversity of a natural population (NP) and two captive broodstocks (SA and SB) of B. orbignyanus. Methods: Samples of caudal fins (NP: 24, SA: 30, and SB: 30) were collected. DNA was extracted and amplified for six RAPD primers and four microsatellite loci. Results: Sixty polymorphic fragments and 17 microsatellite alleles were detected. High intrapopulation heterozygosity (NP: 0.692, SA: 0.724, and SB: 0.686) was observed. Thirty-eight fragments and six alleles were shared among NP, SA, and SB. The FIS and Shannon’s Index of diversity revealed a lack of inbreeding within groups. AMOVA analyses and FST indicated very high (NP vs SA and SB) and small (SA vs SB) genetic differentiation, confirmed by genetic distance and identity, number of migrants and a dendrogram, which revealed the formation of two genetic groups. Conclusions: The two marker types showed similar variability. The groups have adequate genetic variability, with high differentiation between NP and SA–SB, and similarity between broodstocks.Key words: aquaculture, Brycon orbignyanus, genetic conservation, microsatellites, RAPD. ResumenAntecedentes: Piracanjuba (Brycon orbignyanus) es una especie de pez fuertemente impactada por acciones antrópicas como sobrepesca, contaminación del agua y proyectos hidroeléctricos. Esta especie está considerada en peligro de extinción. Objetivo: Analizar la diversidad genética de una población natural (NP) y de dos lotes de reproductores (SA y SB) de B. orbignyanus en cautiverio. Métodos: Se colectaron 84 muestras de aleta caudal (NP: 24, SA: 30 y SB: 30). El ADN fue extraído y amplificado para seis cebadores RAPD y cuatro loci microsatélites. Resultados: Se obtuvieron 60 fragmentos polimórficos y 17 alelos microsatélites. Se observó alta heterocigosidad intra-poblacional (NP: 0,692; SA: 0,724 y SB: 0,686). Treinta y ocho fragmentos y seis alelos fueron compartidos entre NP, SA y SB. Los valores de FIS e índice de Shannon mostraron ausencia de endogamia entre los grupos. Los análisis de ANOVA y FST indicaron alta (NP vs SA y SB) y pequeña (SA vs SB) diferenciación genética; resultados confirmados por la distancia e identidad genética, número de migrantes y dendograma, evidenciando la formación de dos grupos genéticos. Conclusiones: Los grupos poseen adecuada variabilidad genética, con alta diferenciación entre NP vs SA-SB y similitud entre los lotes de reproductores.Palabras clave: acuicultura, Brycon orbignyanus, conservación genética, microsatélites, RAPD. Resumo Antecedentes: Piracanjuba (Brycon orbignyanus) é uma espécie peixe fortemente impactada por ações antrópicas como sobrepesca, poluição e construção de hidrelétricas. Atualmente, essa espécie engloba a lista de peixes que correm perigo de extinção. Objetivo: Analisar a diversidade genética de uma população natural (NP) e de dois estoques de reprodutores em cativeiro (SA e SB) de B. orbignyanus. Métodos: Foram coletadas amostras de nadadeira caudal de 84 indivíduos (NP: 24, SA: 30 e SB: 30). O DNA foi extraido e amplificado para seis primers RAPD e quatro loci microssatélites. Resultados: Foram obtidos 60 fragmentos polimórficos e 17 alelos microssatélites. Foi observada uma alta heterozigosidade intra-populacional (NP: 0,692; SA: 0,724 e SB: 0,686). Trinta e oito fragmentos e seis alelos foram compartilhados entre NP, SA e SB. Os valores de FIS e índice de Shannon demonstraram ausência de endogamia entre os grupos. As análises de AMOVA e FST indicaram alta (NP vs SA e SB) e pequena (SA vs SB) diferenciação genética, resultados confirmados pela distância e identidade genética, número de migrantes e dendrograma, que evidenciaram a formação de dois grupamentos genéticos. Conclusões: Os grupos possuem adequada variabilidade genética, com alta diferenciação entre NP e SA-SB e similaridade entre os estoques de reprodutores.Palabras-chaves: aquicultura, Brycon orbignyanus, conservação genética, microssatélites, RAPD.

Genetic characterization of Markhoz goat breed using microsatellite markers

The use of molecular markers can support the management of endangered populations and should be combined with appropriate breeding strategies to improve productive traits avoiding the decline of the breed. The genetic variability at 10 microsatellite loci were investigated in a sample of 100 unrelated Markhoz goats (77 females and 23 males). The investigated population was reared at the Sanandaj Markhoz goat Performance Testing Station in Kurdistan, Iran. Markhoz goat, a multipurpose breed, is one of the most valuable genetic resources in Iran. All the studied loci were found to be polymorphic and a total number of 52 alleles were identified with an average number of alleles of 5.2. Moreover, some population genetic indices, such as observed and expected heterozygosity, observed and expected number of alleles, Shannon's index, Nei's expected heterozygosity, and polymorphism information content were also calculated. Despite the decreasing population size, Markhoz goat genetic diversity is still conserved. The breed seems to have a good level of genetic variability and, as a consequence, a potential margin of adaptability to environment and for future genetic improvement.