Disentangling the relative influence of bacterioplankton phylogeny and metabolism on lysogeny in reservoirs and lagoons

Previous studies indicate that lysogeny is preponderant when environmental conditions are challenging for the bacterial communities and when their metabolism is reduced. Furthermore, it appears that lysogeny is more frequent within certain bacterial phylogenetic groups. In this comparative study from 10 freshwater reservoirs and 10 coastal lagoons, we aim to disentangle the influence of these different factors. In eight reservoirs and four lagoons, lysogeny was detected by induction assays with mitomycin C, and induction significantly modified the bacterial community composition (BCC), whereas community composition remained constant in ecosystems in which lysogeny was not observed. Among the phylogenetic groups studied, the most abundant ones were Bacteroidetes and α-proteobacteria in lagoons, and β-proteobacteria and Bacteroidetes in reservoirs. These dominant groups comprised the highest proportions of inducible lysogens. In order to unravel the effects of bacterial metabolism from phylogeny on lysogeny, we measured bacterial community physiology and the specific activities of selected phylogenetic groups. The proportion of inducible lysogens within the α- and the β-proteobacteria decreased with increasing group-specific metabolism in lagoons and reservoirs, respectively. In contrast, this relationship was not observed for the other lysogen-containing groups. Hence, both host physiology and phylogeny are critical for the establishment of lysogeny. This study illustrates the importance of lysogeny among the most abundant phylogenetic groups, and further suggests its strong structuring impact on BCC.     

Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes

Genes encoding antirestriction proteins are found in transmissble plasmids (ardABC) and bacteriophage genomes (ocr, darA). Antirestriction proteins inhibit type I restriction-modification enzymes and thus protect the unmodified plasmid or phage DNA from degradation. Antirestriction proteins belong to the family of DNA-mimicry proteins, whose spatial structure mimics the B-form of DNA. Based on an analysis of the mutant forms of ArdA and Ocr obtained by site-directed mutagenesis and the native form of ArdA that specifically inhibit type I restriction enzymes but do not affect their methylase activity, a model is proposed to describe the complex formation between an antirestriction protein and a type I restriction-modification enzyme (R₂M₂S): antirestriction proteins can displace a DNA strand from its binding sites in the S subunit (which contacts a specific site on DNA) and in the R subunit (which translocates the DNA strand and cleaves it). Antirestriction and antimodification activities of ArdA and Ocr as a function of ardA and ocr expression levels were studied by cloning the genes under a strictly regulated promoter.     

Is there more insect folivory in warmer temperate climates? A latitudinal comparison of insect folivory in eastern North America

1.  It is generally believed that warmer climate forests suffer more herbivory, as a proportion of leaf area, than cooler climate forests. However, standardized studies using the same methodology have rarely been performed.
2.  We carried out a study on scattered forest-edge populations of four widespread tree species ( Quercus alba , Acer rubrum , Fagus grandifolia and Liquidambar styraciflua ) spanning 17° of latitude in North America.
3.  We sampled early summer sun leaves (12 weeks after bud break) at each latitude in 2 years. Total insect folivory damage was estimated from the percentage area damaged in fresh leaves on forest edges, using a scanner-linked software.
4.  The percentage area damage per leaf of all four species in both years shows a significant latitudinal trend, with less damage in lower latitude areas of eastern North America. This is contrary to what would generally be expected according to current ecological thinking. Among the four studied species, only A. rubrum showed a significant difference between the 2 years.
5.   Synthesis . The observation of an inverse latitudinal trend may have wider implications for the study of community functioning, suggesting that strength of 'biotic' interaction between plants and herbivores might actually be no less important, or in fact more important, in cool temperate climates compared with warm temperate climates.     

Influence of host and bacteriophage concentrations on the inactivation of food-borne pathogenic bacteria by two phages

To use bacteriophages (phages) to control food-borne pathogenic bacteria, it will be necessary to determine the conditions allowing optimal activity. To start exploring these conditions, a Salmonella phage (P7) and a Campylobacter phage (Cj6) were incubated with their respective hosts at 24 °C for up to 2 h at varying phage and host cell concentrations, and surviving host cells were enumerated. A quadratic polynomial equation was fitted to the inactivation data and contour maps of inactivation against log₁₀ phage and host concentrations were plotted. Inactivation of Salmonella by P7 seemed to be independent of the host concentration, with close to 100% inactivation occurring at a phage concentration of around 5 × 10⁸ PFU mL⁻¹. For Campylobacter phage Cj6, there appeared to be an interaction of both phage and host concentrations. The data obtained were largely consistent with prior work indicating that, at low host cell concentrations, the proportion of cells killed is independent of the host cell concentration. The data indicate that biocontrol of pathogens present in low numbers in liquid foods is achievable, given a sufficiently high concentration of added phages, and that it is not necessary to know the concentration of pathogens to achieve this.     

Significant soil acidification across northern China's grasslands during 1980s–2000s

Anthropogenic acid deposition may lead to soil acidification, with soil buffering capacity regulating the magnitude of any soil pH change. However, little evidence is available from large‐scale observations. Here, we evaluated changes in soil pH across northern China's grasslands over the last two decades using soil profiles obtained from China's Second National Soil Inventory during the 1980s and a more recent regional soil survey during 2001–2005. A transect from the central‐southern Tibetan Plateau to the eastern Inner Mongolian Plateau, where Kriging interpolation provided robust predictions of the spatial distribution of soil pH, was then selected to examine pH changes during the survey period. Our results showed that soil pH in the surface layer had declined significantly over the last two decades, with an overall decrease of 0.63 units (95% confidence interval = 0.54–0.73 units). The decline of soil pH was observed in both alpine grasslands on the Tibetan Plateau and temperate grasslands on the Inner Mongolian Plateau. Soil pH decreased more intensively in low soil carbonate regions, while changes of soil pH showed no significant associations with soil cation exchange capacity. These results suggest that grassland soils across northern China have experienced significant acidification from the 1980s to 2000s, with soil carbonates buffering the increase in soil acidity. The buffering process may induce a large loss of carbon from soil carbonates and thus alter the carbon balance in these globally important ecosystems.     

The impact of temperature on the inactivation of enteric viruses in food and water: a review

Temperature is considered as the major factor determining virus inactivation in the environment. Food industries, therefore, widely apply temperature as virus inactivating parameter. This review encompasses an overview of viral inactivation and virus genome degradation data from published literature as well as a statistical analysis and the development of empirical formulae to predict virus inactivation. A total of 658 data (time to obtain a first log(10) reduction) were collected from 76 published studies with 563 data on virus infectivity and 95 data on genome degradation. Linear model fitting was applied to analyse the effects of temperature, virus species, detection method (cell culture or molecular methods), matrix (simple or complex) and temperature category (<50 and ≥50°C). As expected, virus inactivation was found to be faster at temperatures ≥50°C than at temperatures <50°C, but there was also a significant temperature-matrix effect. Virus inactivation appeared to occur faster in complex than in simple matrices. In general, bacteriophages PRD1 and PhiX174 appeared to be highly persistent whatever the matrix or the temperature, which makes them useful indicators for virus inactivation studies. The virus genome was shown to be more resistant than infectious virus. Simple empirical formulas were developed that can be used to predict virus inactivation and genome degradation for untested temperatures, time points or even virus strains.     

Diversity-dependent stability under mowing and nutrient addition: evidence from a 7-year grassland experiment

Anthropogenic perturbations may affect biodiversity and ecological stability as well as their relationships. However, diversity-stability patterns and associated mechanisms under human disturbances have rarely been explored. We conducted a 7-year field experiment examining the effects of mowing and nutrient addition on the diversity and temporal stability of herbaceous plant communities in a temperate steppe in northern China. Mowing increased population and community stability, whereas nutrient addition had the opposite effects. Stability exhibited positive relationships with species richness at population, functional group and community levels. Treatments did not alter these positive diversity-stability relationships, which were associated with the stabilising effect of species richness on component populations, species asynchrony and portfolio effects. Despite the difficulty of pinpointing causal mechanisms of diversity-stability patterns observed in nature, our results suggest that diversity may still be a useful predictor of the stability of ecosystems confronted with anthropogenic disturbances.     

Succession of bird communities in young temperate rainforests following thinning

We repeated bird and vegetation surveys in 1991–1992 and 2005–2006 among young managed stands and old-growth forests in southeast Alaska to evaluate whether pre-commercial thinning of managed stands influenced the bird community. We compared decadal changes in bird densities and forest vegetation among 3 stand types: managed stands originating from clearcuts 35 years ago that were left untreated (unthinned), managed stands thinned at uniform spacing (thinned), and old growth with no prior timber harvest. We did not detect differences in decadal trends in avian densities between thinned and unthinned stands for 15 of 16 common bird species using a repeated-measures design. Thinning did not result in greater recruitment of overstory-nesting species as predicted. This was likely because of 1) similar increases in tree heights ( = 9–10 m) and canopy cover ( = 29–43%) between unthinned and thinned stands across decades and 2) the relatively young successional stage of these stands, which had only begun to recruit medium and large size conifers (dbh ≥ 36 cm). Decadal trends in densities of most (88%) understory-nesting bird species did not differ between thinned and unthinned stands. Shrub cover decreased by 22% and 31% across decades in thinned and unthinned stands, respectively. Bird community composition in managed stands reflected the general decadal changes in forest vegetation with a shift in dominance from understory species in the early 1990s (80–85% of total bird density) to an equal abundance of understory (45–54%) and overstory species in the mid-2000s. The latter was more similar to old-growth stands, which were dominated by overstory species (67–71%). Overstory-nesting birds in old growth increased in density by 49% across decades. Densities of cavity-nesting species remained unchanged in managed stands and less than densities in old growth across decades, possibly because of a lack of large trees and snags for nest sites. Overall, thinning of clearcut stands, the primary silvicultural system in the region, had few measurable benefits to birds nearly 20 years after treatment. Monitoring over the 70–100-year harvest rotation may be necessary to fully test whether thinning accelerates succession of bird communities in clearcut stands. However, partial harvests that retain large trees and snags should also be explored as alternatives to better maintain late-succession avifauna throughout the harvest rotation in southeast Alaska. © 2012 The Wildlife Society.     

λ噬菌体穿孔素(holin) 蛋白触发裂菌的分子机制

穿孔素-裂解酶二元裂解系统是双链DNA噬菌体普遍采用的裂菌模式,以λ噬菌体为例,系统地揭示了噬菌体穿孔素的结构与功能。λ噬菌体的S基因的特征是呈双起始基序(dual-start motif),编码穿孔素(holin)S105和抗穿孔素(antiholin)S107,通过二者不同水平的表达及相互作用,触发裂菌过程。作者综述了λ噬菌体穿孔素的膜拓扑结构和成孔机制的最新研究进展,并展望了穿孔素的研究热点和应用前景。