Hydrogen ion buffers for biological research

Five new zwitterionic hydrogen ion buffers are described for the first time. These buffers, all N-substituted 3-amino-2-hydroxypropanesulfonic acids, with pK_a's between 6.9 and 7.9 have been subjected to a number of stringent tests in mammalian tissue culture, plant pathology, and virology to detect inhibitory effects. They appear to be equivalent to or better than any other buffers heretofore available.     

Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements

Background  

Environmental ozone can rapidly degrade cyanine 5 (Cy5), a fluorescent dye commonly used in microarray gene expression studies. Cyanine 3 (Cy3) is much less affected by atmospheric ozone. Degradation of the Cy5 signal relative to the Cy3 signal in 2-color microarrays will adversely reduce the Cy5/Cy3 ratio resulting in unreliable microarray data.     

The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.Subject terms: Microbial ecology, Community ecology     

Seasonal effects of 19 plant species on COD removal in subsurface treatment wetland microcosms

Plants have many well-documented influences in treatment wetlands, but differences in individual species’ effects on year-round and seasonal performance are poorly understood. In this study, we evaluated plant effects on seasonal patterns of organic carbon removal (measured as COD) and sulfate concentration (used as an indicator of rootzone oxidation) in replicated, batch-loaded, greenhouse microcosms simulating subsurface treatment wetlands. Microcosms were planted with monocultures of 19 plant species or left unplanted as controls, dosed every 20 days with synthetic secondary wastewater, and operated over 20 months at temperatures from 4 to 24 °C. Study-long COD removal averaged 70% for controls and 70-97% for individual species. Most species enhanced COD removal significantly and the benefits of plants were greatest at 4-8 °C because COD removal decreased at low temperatures in controls but displayed limited seasonal variation in planted microcosms. Removal was significantly better at 24 °C than 4 °C with two species (Panicum virgatum and Leymus cinereus), significantly poorer with two species (Carex utriculata and Phalaris arundinacea), and did not differ with 15 species. Only one species showed a significant positive correlation between temperature and COD removal (Iris missouriensis, r = 0.67), while two species showed significant negative correlations (better when colder: Carex nebrascensis, r = −0.67; C. utriculata, r = −0.93). High COD removal throughout the study was strongly associated with high SO₄ concentrations at low temperatures, suggesting that plant performance is related to rootzone oxidation and species’ abilities to promote aerobic over anaerobic microbial processes, particularly in winter. Results indicate that improved year-round and cold-season COD removal is common across diverse wetland plant species and novel species can be as good or better than those typically used. Better performing species were largely in the sedge and rush families (Cyperaceae and Juncaceae), while poorer performing species were largely in the grass family (Poaceae).