Two modes of evolution shape bacterial strain diversity in the gut for thousands of generations

How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show that gut environments can rapidly generate diversifying selection and ecotype formation.

Contribution of tiller age category to herbage accumulation of Marandu palisadegrass under two fertilization regimes

Based on the hypothesis that climate and fertilizers influence the proportion of tiller age categories in the canopy and, consequently, in herbage accumulation, the objective of this study was to determine the population density and the contribution of tiller age categories for herbage accumulation of Urochloa brizantha cv. Marandu during the year and in response to phosphate and nitrogen fertilization. The treatments consisted of two fertilization strategies: low and high fertilization and three tiller ages (young, mature and old), evaluated at four times of the year: winter, early and late spring, and summer. The total number of tillers and the proportion of young tillers were higher in late spring and summer. The growth and herbage accumulation rates showed a typical seasonal pattern and were higher in the canopy under high fertilization. Old tillers contributed more to control the total stem growth rate, as well as the canopy senescence rate. The highest percentage of young tillers is related to the high herbage accumulation in the Marandu palisadegrass canopy.

Dryland irrigation increases accumulation rates of pedogenic carbonate and releases soil abiotic CO2

Agricultural fields in drylands are challenged globally by limited freshwater resources for irrigation and also by elevated soil salinity and sodicity. It is well known that pedogenic carbonate is less soluble than evaporate salts and commonly forms in natural drylands. However, few studies have evaluated how irrigation loads dissolved calcium and bicarbonate to agricultural fields, accelerating formation rates of secondary calcite and simultaneously releasing abiotic CO2 to the atmosphere. This study reports one of the first geochemical and isotopic studies of such “anthropogenic” pedogenic carbonates and CO2 from irrigated drylands of southwestern United States. A pecan orchard and an alfalfa field, where flood-irrigation using the Rio Grande river is a common practice, were compared to a nearby natural dryland site. Strontium and carbon isotope ratios show that bulk pedogenic carbonates in irrigated soils at the pecan orchard primarily formed due to flood-irrigation, and that approximately 20–50% of soil CO2 in these irrigated soils is calcite-derived abiotic CO2 instead of soil-respired or atmospheric origins. Multiple variables that control the salt buildup in this region are identified and impact the crop production and soil sustainability regionally and globally. Irrigation intensity and water chemistry (irrigation water quantity and quality) dictate salt loading, and soil texture governs water infiltration and salt leaching. In the study area, agricultural soils have accumulated up to 10 wt% of calcite after just about 100 years of cultivation. These rates will likely increase in the future due to the combined effects of climate variability (reduced rainfall and more intense evaporation), use of more brackish groundwater for irrigation, and reduced porosity in soils. The enhanced accumulation rates of pedogenic carbonate are accompanied by release of large amounts of abiotic CO2 from irrigated drylands to atmosphere. Extensive field studies and modelling approaches are needed to further quantify these effluxes at local, regional and global scales.

Assessing controls on organic matter enrichments in hemipelagic homogenous marls of the Cretaceous Vocontian Basin (France): an unexpected variability observed from multiple organic-rich levels

The Marnes Bleues Formation from the Vocontian Basin (Southeastern France) shows many organic rich levels, some concomitant to oceanic anoxic events OAE1a and OAE1b. These organic-rich levels are scattered through a thick homogeneous succession of marls, poor in organic matter (OM). Through a multi-parameter approach, the organic-rich levels from the Aptian-Albian were characterized. Our results show that all OM-rich levels exhibit variable characteristics, such as OM nature (marine vs. continental), sedimentation and accumulation rates, redox conditions, surface-water productivity and relative sea level, but they all show low to modest enrichments in OM. Furthermore, all the levels share in common the fact that they formed under conditions of normal to low productivity and oxic to suboxic conditions. Thus, our results strongly suggest that, in the absence of high productivity and anoxic bottom conditions, the other factors reputed to favor OM accumulation only led to sporadic and low enrichments in organic contents. It is as if such factors could only enhance OM accumulation but could not induce it alone. What was true for the Vocontian Basin may be extended to other settings, regardless of their time of deposition or location.

Carbon accumulation rates of Holocene peatlands in central–eastern Europe document the driving role of human impact over the past 4000 years

Peatlands are one of the largest terrestrial carbon sinks on the planet, yet little is known about the carbon accumulation rates (CARs) of mountainous peatlands. The long-term variability in the size of the associated carbon sink and its drivers remain largely unconstrained, especially when the long-term anthropogenic impact is also considered. Here, we present a composite CAR record of nine peatlands from central–eastern Europe (Romania and Serbia) detailing variability in the rates of carbon accumulation during the Holocene. We show examples of extremely high long-term rates of carbon accumulation (LORCA>120 gCm-2yr-1), indicating that mountain peatlands constitute an efficient regional carbon sink at times. By comparing our data to modelled palaeoclimatic indices and to measures of anthropogenic impact we disentangle the drivers of peat carbon accumulation in the area. Variability in early- and mid-Holocene CARs is linked to hydroclimatic controls, with high CARs occurring during the early Holocene and lower CARs associated with the transition to cooler and moister mid-Holocene conditions. By contrast, after 4000 years (calibrated) before present (years BP), the trends in CARs indicate a divergence from hydroclimate proxies, suggesting that other processes became the dominant drivers of peat CARs. We propose that enhanced erosion following tree cover reduction as well as increased rates of long-distance atmospheric dust fallout might have played a role, as both processes would result in enhanced mineral and nutrient supply to bog surfaces, stimulating peatland productivity. Surprisingly though, for the last 1000 years, reconstructed temperature is significantly correlated with CARs, with rising temperatures linked to higher CARs. Under future climate conditions, which are predicted to be warmer in the region, we predict that peat growth may expand but that this is entirely dependent upon the scale of human impact directly affecting the sensitive hydrological budget of these peatlands.

Mercury accumulation in leaves of different plant types – the significance of tissue age and specific leaf area

Mercury, Hg, is one of the most problematic metals from an environmental perspective. To assess the problems caused by Hg in the environment, it is crucial to understand the processes of Hg biogeochemistry, but the exchange of Hg between the atmosphere and vegetation is not sufficiently well characterized. We explored the mercury concentration, [Hg], in foliage from a diverse set of plant types, locations and sampling periods to study whether there is a continuous accumulation of Hg in leaves and needles over time. Measurements of [Hg] were made for deciduous and conifer trees in Gothenburg, Sweden (botanical garden and city area), as well as for evergreen trees in Rwanda. In addition, data for wheat from an ozone experiment conducted at Östad, Sweden, were included. Conifer data were quantitatively compared with literature data. In every case where older foliage was directly compared with younger, [Hg] was higher in older tissue. Covering the range from the current year up to 4-year-old needles in the literature data, there was no sign of Hg saturation in conifer needles with age. Thus, over timescales of approximately 1 month to several years, the Hg uptake in foliage from the atmosphere always dominated over Hg evasion. Rwandan broadleaved trees had generally older leaves due to lack of seasonal abscission and higher [Hg] than Swedish broadleaved trees. The significance of atmospheric Hg uptake in plants was shown in a wheat experiment where charcoal-filtrated air led to significantly lower leaf [Hg]. To search for general patterns, the accumulation rates of Hg in the diverse set of tree species in the Gothenburg area were related to the specific leaf area (SLA). Leaf-area-based [Hg] was negatively and non-linearly correlated with SLA, while mass-based [Hg] had a somewhat weaker positive relationship with SLA. An elaborated understanding of the relationship behind [Hg] and SLA may have the potential to support large-scale modelling of Hg uptake by vegetation and Hg circulation.