Effect of diet modification in intestinal Escherichia coli population and antimicrobial resistance

The fluctuations in the number of some intestinal bacterial lineages may be associated with increased antimicrobial resistance and disease. Adaptation to a given environment may select bacterial mutants that have reduced ability to adapt to new environments and changes in diet have been associated with alterations in microbiome taxon composition. We wanted to see the effect of diet change in linage composition and antimicrobial resistance profiles of numerically dominant E. coli. We subjected 50 chickens from an industrial operation (under corn-based diet supplemented with antimicrobials) to 2 antimicrobial-free diets; one based on corn and the other based on alfalfa. Fecal samples were obtained from all animals at arrival and after five weeks under different diets. Five E. coli colonies (from each sample) were subjected to genetic typing and antimicrobial susceptibility testing. We observed high diversity and high turnover rate of numerically dominant E. coli strains from animals from both diet groups. We did not find differences in antimicrobial resistance profiles in isolates from different diet groups. Our results suggest that there is high diversity and high turnover rate of E. coli strains in the intestines regardless of the diet. Chicken intestines seemed to contain many E. coliThe fluctuations in the number of some intestinal bacterial lineages may be associated with increased antimicrobial resistance and disease. Adaptation to a given environment may select bacterial mutants that have reduced ability to adapt to new environments and changes in diet have been associated with alterations in microbiome taxon composition. We wanted to see the effect of diet change in linage composition and antimicrobial resistance profiles of numerically dominant E. coli. We subjected 50 chickens from an industrial operation (under corn-based diet supplemented with antimicrobials) to 2 antimicrobial-free diets; one based on corn and the other based on alfalfa. Fecal samples were obtained from all animals at arrival and after five weeks under different diets. Five E. coli colonies (from each sample) were subjected to genetic typing and antimicrobial susceptibility testing. We observed high diversity and high turnover rate of numerically dominant E. coli strains from animals from both diet groups. We did not find differences in antimicrobial resistance profiles in isolates from different diet groups. Our results suggest that there is high diversity and high turnover rate of E. coli strains in the intestines regardless of the diet. Chicken intestines seemed to contain many E. coli lineages able to thrive in different substrates. The absence of differences in antimicrobial resistance among bacteria, from animals in different diets, may indicate that the carriage of antimicrobial resistance genes does not affect the bacterial ability to adapt to different substrates. lineages able to thrive in different substrates. The absence of differences in antimicrobial resistance among bacteria, from animals in different diets, may indicate that the carriage of antimicrobial resistance genes does not affect the bacterial ability to adapt to different substrates.

Benthic Macroinvertebrates In Streams Contaminated By Acid Mine Drainage – A Pilot Study From Thailand

Benthic macroinvertebrates were sampled by a D-Frame Dip net (450 µm mesh size) from 3 sites of a stream contaminated with acid mine drainage from a gold mine in Loei Province, Thailand. Sialis larvae (Insecta: Megaloptera: Sialidae) were dominant taxa (49%) in the high Arsenic upstream site 1 followed by dipteran larvae (26%), gastropods (15%) and Coleoptera (10%). The less contaminated, downstream site 3 was dominated by Coleoptera (32%), Ephemeroptera nymphs (24%) and Caridina (F. Atyidae, O. Decapoda-20%). Seventeen percent of mouthpart deformity of chironomid larvae was also found in site 2. It is preliminary concluded that the extent of contamination with mining waste water has affected both, taxon composition and the proportion of chironomids with deformed mouth parts.

Planktonic Foraminifera as Oceanographic Proxies: Comparison of Biogeographic Classifications Using Some Southwest Pacific Core-Top Faunas

The distribution of planktonic foraminifera, as free-floating protists, is largely controlled by hydrography. Their death assemblages in surficial sediments provide proxy data on upper water mass properties for paleoceanography. Techniques for mapping faunal distributions for this purpose are compared in a study of 35 core-top samples that span the Subtropical Front in the Southwest Pacific. Faunas are analyzed by taxon composition, order of dominant taxa, and abundance. Taxon composition (presence-absence data) and dominant taxa (ordinal data) recognize groups of sites that approximate major water mass distributions (cool subtropical water, subantarctic water) and clearly define the location of the Subtropical Front. Quantitative data (relative abundances) more closely reflect the success of taxa in upper water mass niches. This information resolves groups of sites that reflect differences in intrawater mass hydrography. Comparisons suggest that abundance data should provide much better oceanographic resolution globally than the widely used ordinal biogeographic classification that identifies only Tropical, Subtropical Transitional, Subpolar and Polar provinces. As the data are strongly structured by variance in the abundance of Globigerina bulloides, Globorotalia inflata, Neogloboquadrina incompta, and Neogloboquadrina pachyderma, comparable classifications result from most clustering strategies. Principal coordinates analysis best represents the configuration of sites in two dimensions.

Archaeal Assemblages Inhabiting Temperate Mixed Forest Soil Fluctuate in Taxon Composition and Spatial Distribution over Time

This study explored the persistence and spatial distribution of a diverse Archaeal assemblage inhabiting a temperate mixed forest ecosystem. Persistence under native conditions was measured from 2001 to 2010, 2011, and 2012 by comparison of 16S rRNA gene clone libraries. The Archaeal assemblages at each of these time points were found to be significantly different (AMOVA,P<0.01), and the nature of this difference was dependent on taxonomic rank. For example, the cosmopolitan genus g_Ca.Nitrososphaera (I.1b) was detected at all time points, but within this taxon the abundance of s_SCA1145, s_SCA1170, and s_Ca.N. gargensis fluctuated over time. In addition, spatial heterogeneity (patchiness) was measured at these time points using 1D TRFLP-SSCP fingerprinting to screen soil samples covering multiple spatial scales. This included soil collected from small volumes of 3 cubic centimeters to larger scales—over a surface area of 50 m2, plots located 1.3 km apart, and a separate locality 23 km away. The spatial distribution of Archaea in these samples changed over time, and while g_Ca.Nitrososphaera (I.1b) was dominant over larger scales, patches were found at smaller scales that were dominated by other taxa. This study measured the degree of change for Archaeal taxon composition and patchiness over time in temperate mixed forest soil.

Spatial distribution of forest landscape change in western New York from presettlement to the present

Changes in tree taxon composition and distribution in western New York over a 200 year time period ca. 1797–1993 were examined by comparing the presettlement land survey with the US Forest Inventory and Analysis (FIA) survey. To ensure data quality, biases in presettlement bearing tree selection and FIA plot location were assessed. A 6 mile × 6 mile grid of taxa abundance was then estimated using geostatistics. Overall, significant changes in taxon composition occurred, with the taxa most abundant in the presettlement land survey — beech (37.0%), sugar maple (21.0%), and eastern hemlock (8.3%) — being replaced by sugar maple (19.2%), ash (11.7%), and red maple (11.4%) in the FIA survey. Spatially resolved comparisons showed that the landscape changed from fairly spatially homogeneous to more heterogeneous; in the presettlement survey, the most abundant taxon in most of the 6 mile × 6 mile grid cells was beech, while in the present survey, the most abundant taxon in most of the cells was one of several early successional taxa that each displayed a distinctly clustered geographic pattern of dominance. The clusters of dominance of the different early successional taxa may correspond to environmental factors. This study demonstrates the insights available through spatially resolved analyses of changes in the forest landscape between presettlement and present.

Spatial, environmental and anthropogenic effects on the taxon composition of hybridizing Daphnia

The competitive ability of hybrids, compared with their parental taxa, can cover a wide fitness range from poor to superior. For example communities of the Daphnia galeata – hyalina – cucullata species complex often show hybrid dominance. We tested whether taxa composition of 43 European lakes inhabited by this species complex can be explained by habitat characteristics (e.g. size descriptors, trophy level) or geography. We found that D. galeata occurs more frequently south of the Alps, whereas D. hyalina and D. cucullata are found more in the north. Lakes with D. galeata dominance had higher temperatures whereas D. hyalina dominance could be attributed to low phosphorus loads. The dominance of F 1 -hybrids, however, was not explainable with current environmental variables. In a subset of 28 lakes, we studied the impact of eutrophication history on F 1 -hybrid success. Lakes with the highest trophic state in the past tended to be dominated by F 1 -hybrids. Our data demonstrate that human-mediated habitat disturbance (eutrophication) has facilitated hybrid success and altered the Daphnia taxon composition across lakes. At the same time, specific habitat conditions might provide a refuge from hybridization for native genotypes.