Survival of a microbial inoculant in soil after recurrent inoculations.

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

Graded SiGe waveguides with broadband low-loss propagation in the mid infrared.

Mid-infrared (mid-IR) silicon photonics is expected to lead key advances in different areas including spectroscopy, remote sensing, nonlinear optics or free-space communications, among others. Still, the inherent limitations of the silicon-on-insulator (SOI) technology, namely the early mid-IR absorption of silicon oxide and silicon at λ~3.6 µm and at λ ~8.5 µm respectively, remain the main stumbling blocks that prevent this platform to fully exploit the mid-IR spectrum (λ ~2-20 µm). Here, we propose using a compact Ge-rich graded-index Si1-xGex platform to overcome this constraint. A flat propagation loss characteristic as low as 2-3 dB/cm over a wavelength span from λ = 5.5 µm to 8.5 µm is demonstrated in Ge-rich Si1-xGex waveguides of only 6 µm thick. The comparison of three different waveguides design with different vertical index profiles demonstrates the benefit of reducing the fraction of the guided mode that overlaps with the Si substrate to obtain such flat low loss behavior. Such Ge-rich Si1-xGex platforms may open the route towards the implementation of mid-IR photonic integrated circuits with low-loss beyond the Si multi-phonon absorption band onset, hence truly exploiting the full Ge transparency window up to λ ~15 µm.

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.

Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.

Ge-rich graded-index Si1-xGex waveguides with broadband tight mode confinement and flat anomalous dispersion for nonlinear mid-infrared photonics.

This work explores the use of Ge-rich graded-index Si1-xGex rib waveguides as building blocks to develop integrated nonlinear optical devices for broadband operation in the mid-IR. The vertical Ge gradient concentration in the waveguide core renders unique properties to the guided optical mode, providing tight mode confinement over a broadband mid-IR wavelength range from λ = 3 µm to 8 µm. Additionally, the gradual vertical confinement pulls the optical mode upwards in the waveguide core, overlapping with the Ge-rich area where the nonlinear refractive index is larger. Moreover, the Ge-rich graded-index Si1-xGex waveguides allow efficient tailoring of the chromatic dispersion curves, achieving flat anomalous dispersion for the quasi-TM optical mode with D ≤ 14 ps/nm/km over a ~1.4 octave span while retaining an optimum third-order nonlinear parameter, γeff. These results confirm the potential of Ge-rich graded-index Si1-xGex waveguides as an attractive platform to develop mid-IR nonlinear approaches requiring broadband dispersion engineering.

High quality entanglement on a chip-based frequency comb.

We report an efficient energy-time entangled photon-pair source based on four-wave mixing in a CMOS-compatible silicon photonics ring resonator. Thanks to suitable optimization, the source shows a large spectral brightness of 400 pairs of entangled photons /s/MHz for 500 µW pump power, compatible with standard telecom dense wavelength division multiplexers. We demonstrate high-purity energy-time entanglement, i.e., free of photonic noise, with near perfect raw visibilities (> 98%) between various channel pairs in the telecom C-band. Such a compact source stands as a path towards more complex quantum photonic circuits dedicated to quantum communication systems.

Low loss 40 Gbit/s silicon modulator based on interleaved junctions and fabricated on 300 mm SOI wafers.

We demonstrate high-speed silicon modulators based on carrier depletion in interleaved pn junctions fabricated on 300 mm-SOI wafers using CMOS foundry facilities. 950 µm-long Mach Zehnder (MZ) and ring resonator (RR) modulator with a 100 µm radius, were designed, fabricated and characterized. 40 Gbit/s data transmission has been demonstrated for both devices. The MZ modulator exhibited a high extinction ratio of 7.9 dB with only 4 dB on-chip losses at the operating point.

Unraveling the effects of management regime and plant species on soil organic carbon and microbial phospholipid fatty acid profiles in grassland soils.

In a field experiment we have examined the effect of long-term grassland management regimes (viz., intensive versus extensive) and dominant plant species (viz., Arrhenatherum elatius, Holcus lanatus and Dactylis glomerata) on soil organic carbon (SOC) build up, soil microbial communities using biomarker phospholipid fatty acids (PLFA), and the relationship between SOC and PLFAs of major groups of microorganisms (viz., bacteria, fungi, and actinomycetes). The results have revealed that changes in SOC were not significantly affected by the intensity of management or by the plant species composition or by their interaction. The amount of PLFA of each microbial group was affected weakly by management regime and plant species, but the canonical variance analysis (CVA), based on individual PLFA values, demonstrated significant (P<0.05) effects of management regime and plant species on the composition of microbial community. Positive and significant (P<0.01) relationships were observed between PLFA of bacteria (R2=0.47), fungi (R2=0.33), actinomycetes (R2=0.71) and total microbial PLFA (R2=0.53) and SOC content.

Does variability in shoot carbon assimilation within the tree crown explain variability in peach fruit growth?

A three-dimensional model of radiative transfer and leaf gas exchange was used to quantify daily carbon (C) assimilation of all fruit-bearing shoots (FBS) in an early maturing 6-year-old peach tree (Prunus persica L. Batsch) with a heavy crop load. For a sample of FBS (n=36), growth of fruit and leafy shoots was measured every 1-2 weeks from 24 days after bloom (DAB) until harvest, between 93-101 DAB. The objective was to relate shoot C assimilation with harvested fruit mass for each shoot to test the hypothesis that variation in C supply contributes significantly to variation in fruit growth within and among FBS. Mean C assimilation of the sampled shoots was 0.07 g C fruit(-1) day(-1), but varied between 0.014 and 0.32 g C fruit(-1) day(-1). This indicates that C availability for fruit growth would have varied significantly among individual FBS if they were autonomous. Mean fruit dry mass on each FBS varied between 0.716 and 7.68 g C at harvest, and most of the variation originated among, not within, individual FBS. However, there were no correlations between the mean and standard deviation of fruit mass and fruit relative growth rate when each was plotted against shoot C assimilation, indicating that factors such as those regulating C demand of fruit, or C transfer among individual FBS, may be more important in controlling variability in fruit growth than intra-crown variability in shoot C assimilation. Under the study conditions, FBS were non-autonomous for C, because a model of fruit and leafy shoot growth was unable to reproduce the observed growth without supplementary contribution of C from shoots without fruit.

Stimulation of soil nitrification and denitrification by grazing in grasslands: do changes in plant species composition matter?

Stimulation of nitrification and denitrification by long term (from years to decades) grazing has commonly been reported in different grassland ecosystems. However, grazing generally induces important changes in plant species composition, and whether changes in nitrification and denitrification are primarily due to changes in vegetation composition has never been tested. We compared soil nitrification- and denitrification-enzyme activities (NEA and DEA, respectively) between semi-natural grassland sites experiencing intensive (IG) and light (LG) grazing/mowing regimes for 13 years. Mean NEA and DEA (i.e. observed from random soil sampling) were higher in IG than LG sites. The NEA/DEA ratio was higher in IG than LG sites, indicating a higher stimulation of nitrification. Marked changes in plant species composition were observed in response to the grazing/mowing regime. In particular, the specific phytomass volume of Elymus repens was lower in IG than LG sites, whereas the specific volume of Lolium perenne was higher in IG than LG sites. In contrast, the specific volume of Holcus lanatus, Poa trivialis and Arrhenatherum elatius were not significantly different between treatments. Soils sampled beneath grass tussocks of the last three species exhibited higher DEA, NEA and NEA/DEA ratio in IG than LG sites. For a given grazing regime, plant species did not affect significantly soil DEA, NEA and NEA/DEA ratio. The modification of plant species composition is thus not the primary factor driving changes in nitrification and denitrification in semi-natural grassland ecosystems experiencing long term intensive grazing. Factors such as trampling, N returned in animal excreta, and/or modification of N uptake and C exudation by frequently defoliated plants could be responsible for the enhanced microbial activities.

A biochemical model of photosynthesis for mango leaves: evidence for the effect of fruit on photosynthetic capacity of nearby leaves.

Variations in leaf nitrogen concentration per unit mass (Nm) and per unit area (Na), mass-to-area ratio (Ma), total nonstructural carbohydrates (Ta), and photosynthetic capacity (maximum carboxylation rate, electron transport capacity, rate of phosphate release in triose phosphate utilization and dark respiration rate) were studied within the digitized crowns of two 3-year-old mango trees (Mangifera indica L.) on La Réunion Island. Additional measurements of Nm, Na, Ma, Ta and photosynthetic capacities were performed on young, fully expanded leaves of 11-year-old mango trees. Leaves of similar gap fractions were taken far from and close to developing fruits. Unlike Nm, both Na and Ta were linearly correlated to gap fraction. Similar relationships were found for all leaves whatever their age and origin, except for Ta, for which we found a significant tree effect. Photosynthetic capacity was nonlinearly correlated to Na, and a unique relationship was obtained for all types of leaves. Photosynthetic acclimation to light was mainly driven by changes in Ma, but allocation of total leaf N between the different photosynthetic functions also played a substantial role in acclimation to the lowest irradiances. Leaves close to developing fruits exhibited a higher photosynthetic capacity than other leaves, but similar Ta. Our data suggest that Ta does not control photosynthetic capacity in mango leaves. We used the data to parameterize a biochemically based model of photosynthesis and an empirical stomatal conductance model, allowing accurate predictions of net photosynthesis of leaves in field-grown mango trees.

Photosynthetic light acclimation in peach leaves: importance of changes in mass:area ratio, nitrogen concentration, and leaf nitrogen partitioning.

Photosynthetic light acclimation of leaves can result from (i) changes in mass-based leaf nitrogen concentration, Nm, (ii) changes in leaf mass:area ratio, Ma, and (iii) partitioning of total leaf nitrogen among different pools of the photosynthetic machinery. We studied variations in Nm and Ma within the crowns of two peach (Prunus persica L. Batsch) trees grown in an orchard in Portugal, and one peach tree grown in an orchard in France. Each crown was digitized and a 3-D radiation transfer model was used to quantify the intra-crown variations in time-integrated leaf irradiance, . Nitrogen concentration, leaf mass:area ratio, chlorophyll concentration, and photosynthetic capacity were also measured on leaves sampled on five additional peach trees in the orchard in Portugal. The data were used to compute the coefficients of leaf nitrogen partitioning among carboxylation, bioenergetics, and light harvesting pools. Leaf mass:area ratio and area-based leaf nitrogen concentration, Na, were nonlinearly related to , and photosynthetic capacity was linearly related to Na. Photosynthetic light acclimation resulted mainly from changes in Ma and leaf nitrogen partitioning, and to a lesser extent from changes in Nm. This behavior contrasts with photosynthetic light acclimation observed in other tree species like walnut (Juglans regia L.) in which acclimation results primarily from changes in Ma.

Temperature response of leaf photosynthetic capacity in seedlings from seven temperate tree species.

Seedlings of seven temperate tree species (Acer pseudoplatanus L., Betula pendula Roth, Fagus sylvatica L., Fraxinus excelsior L., Juglans regia L., Quercus petraea Matt. Liebl. and Quercus robur L.) were grown in a nursery under neutral filters transmitting 45% of incident global irradiance. During the second or third year of growth, leaf photosynthetic capacity (i.e., maximal carboxylation rate, Vcmax, maximal photosynthetic electron transport rate, Jmax, and dark respiration, Rd) was estimated for five leaves from each species at five or six leaf temperatures (10, 18, 25, 32, 36 and 40 degrees C). Values of Vcmax and Jmax were obtained by fitting the equations of the Farquhar model on response curves of net CO2 assimilation (A) to sub-stomatal CO2 mole fraction (ci), at high irradiance. Primary parameters describing the kinetic properties of Rubisco (specificity factor, affinity for CO2 and for O2, and their temperature responses) were taken from published data obtained with spinach and tobacco, and were used for all species. The temperature responses of Vcmax and Jmax, which were fitted to a thermodynamic model, differed. Mean values of Vcmax and Jmax at a reference temperature of 25 degrees C were 77.3 and 139 micromol m(-2) s(-1), respectively. The activation energy was higher for Vcmax than for Jmax (mean values of 73.1 versus 57.9 kJ mol(-1)) resulting in a decrease in Jmax/Vcmax ratio with increasing temperature. The mean optimal temperature was higher for Vcmax than for Jmax (38.9 versus 35.9 degrees C). In addition, differences in these temperature responses were observed among species. Temperature optima ranged between 35.9 and above 45 degrees C for Vcmax and between 31.7 and 43.3 degrees C for Jmax, but because of data scatter and the limited range of temperatures tested (10 to 40 degrees C), there were few statistically significant differences among species. The optimal temperature for Jmax was highest in Q. robur, Q. petraea and J. regia, and lowest in A. pseudoplatanus and F. excelsior. Measurements of chlorophyll a fluorescence revealed that the critical temperature at which basal fluorescence begins to increase was close to 47 degrees C, with no difference among species. These results should improve the parameterization of photosynthesis models, and be of particular interest when adapted to heterogeneous forests comprising mixtures of species with diverse ecological requirements.

Spatial distribution of leaf dry weight per area and leaf nitrogen concentration in relation to local radiation regime within an isolated tree crown.

To assess the spatial distribution of photosynthetic capacity within an isolated 20-year-old walnut tree (Juglans regia L.) crown, the distribution of relevant leaf characteristics was measured. Variations in leaf dry weight per area (W(a)), and nitrogen content on a weight (N(w)) and area basis (N(a)) were studied along two horizontal and one vertical gradients of leaf irradiance, at two dates (July 30 and September 3). In addition, the content of total nonstructural carbon on a weight (TNC(w)) and area basis (TNC(a)) was measured on July 30. Concurrently, the spatial distribution of daily integrated leaf irradiance within the crown was simulated by a three-dimensional radiation transfer model over a one week period before sampling at each date. High spatial heterogeneity was observed for W(a) (from 50 to 140 g m(-2)), TNC(a) (from 4 to 17 g m(-2)) and N(a) (from 1.2 to 3.6 g m(-2)) among the foliage. Although TNC(w) and N(w) were not correlated and only weakly correlated to daily leaf irradiance, respectively, W(a), TNC(a) and N(a) were strongly correlated to daily leaf irradiance. The relationship between observed N(a) and simulated daily leaf irradiance was used to assess the spatial distribution of N(a) within the crown at each date. Total leaf nitrogen in the foliage was estimated to be 339 g in late July and 317g in early September. For the whole crown (i.e., 1729 current-year shoots), N(a) increased strongly with basal shoot diameter (an index of "shoot vigor"), highlighting the fact that large shoots were mainly located in sunlit locations and exhibited high photosynthetic capacity.

Spatial partitioning of the soil water resource between grass and shrub components in a West African humid savanna.

Most savanna water balance models assume water partitioning between grasses and shrubs in a two-layer hypothesis, but this hypothesis has not been tested for humid savanna environments. Spatial partitioning of soil water between grasses and shrubs was investigated in a West African humid savanna by comparing the isotopic composition (oxygen-18 and deuterium) of soil water and plant stem water during rainy and dry conditions. Both grass and shrub species acquire most of their water from the top soil layer during both rainy and dry periods. A shift of water uptake pattern towards deeper horizons was observed only at the end of the dry season after shrub defoliation. The mean depth of water uptake, as determined by the isotopic signature of stem water, was consistent with grass and shrub root profiles and with changes in soil water content profiles as surveyed by a neutron probe. This provides evidence for potentially strong competition between shrubs and grasses for soil water in these humid savannas. Limited nutrient availability may explain these competitive interactions. These results enhance our understanding of shrub-grass interactions, and will contribute to models of ecosystem functioning in humid savannas.