Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana.

In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.

Plant-soil synchrony in nutrient cycles: Learning from ecosystems to design sustainable agrosystems.

Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant-soil and plant-plant interactions, eco-physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2 O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature-based practices allowing for site-specific modifications. This new synthetized knowledge should help practitioners to improve the long-term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate.

Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition.

The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils across the Tibet plateau, with distances among plots ranging from 20 m to 1550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Factors representing climate, soil and plant community were measured to assess different facets of environmental dissimilarity. Both bacterial taxonomic and functional dissimilarities were more related to abiotic dissimilarity than biotic (vegetation) dissimilarity or distance. Taxonomic dissimilarity was mostly explained by differences in soil pH and mean annual temperature (MAT), while functional dissimilarity was linked to differences in soil N and P availabilities and N:P ratio. Soil pH and MAT remained the main determinants of taxonomic dissimilarity across spatial scales. In contrast, the explanatory variables of N-related functional dissimilarity varied across the scales, with soil moisture and organic matter having the highest role across short distances (<~330 km), and available P, N:P ratio and distance being important over long distances (>~660 km). Our results demonstrate how biodiversity dimension (taxonomic versus functional aspects) and spatial scale influence the factors driving soil bacterial biogeography.

Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.

Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2 ), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.

Broadband behavior of quadratic metalenses with a wide field of view.

Metalenses are attracting a large interest for the implementation of complex optical functionalities in planar and compact devices. However, chromatic and off-axis aberrations remain standing challenges. Here, we experimentally investigate the broadband behavior of metalenses based on quadratic phase profiles. We show that these metalenses do not only guarantee an arbitrarily large field of view but are also inherently tolerant to longitudinal and transverse chromatic aberrations. As such, we demonstrate a single-layer, silicon metalens with a field of view of 86° and a bandwidth up to 140 nm operating at both 1300 nm and 1550 nm telecommunication wavelength bands.

Strong pump rejection filter for polarization-diverse silicon platforms.

Integrated wavelength filters with high optical rejection are key components in several silicon photonics circuits, including quantum photon-pair sources and spectrometers. Non-coherent cascading of modal-engineered Bragg filters allows for remarkable optical rejections in structures that only support transverse-electric (TE) polarized modes such as uncladded 220-nm-thick silicon. However, the restriction to TE-only platforms limits the versatility of the non-coherent cascading approach. Here, we propose and experimentally demonstrate a new, to the best of our knowledge, approach for high-rejection filters in polarization-diverse platforms by combining non-coherent cascading of modal-engineered Bragg filters and anisotropy-engineered metamaterial bends. Bragg filters provide a high rejection of the TE mode, while the metamaterial bends remove any residual power propagating in the transverse-magnetic (TM) mode, without any penalty in terms of insertion loss or device footprint. Based on this strategy, we demonstrate optical rejection exceeding 60 dB in 300-nm-thick, cladded silicon waveguides.

Mid-infrared Fourier-transform spectrometer based on metamaterial lateral cladding suspended silicon waveguides.

Integrated mid-infrared micro-spectrometers have a great potential for applications in environmental monitoring and space exploration. Silicon-on-insulator (SOI) is a promising platform to tackle this integration challenge, owing to its unique capability for large volume and low-cost production of ultra-compact photonic circuits. However, the use of SOI in the mid-infrared is restricted by the strong absorption of the buried oxide layer for wavelengths beyond 4 µm. Here, we overcome this limitation by utilizing metamaterial-cladded suspended silicon waveguides to implement a spatial heterodyne Fourier-transform (SHFT) spectrometer operating at wavelengths near 5.5 µm. The metamaterial-cladded geometry allows removal of the buried oxide layer, yielding measured propagation loss below 2 dB/cm at wavelengths between 5.3 and 5.7 µm. The SHFT spectrometer comprises 19 Mach-Zehnder interferometers with a maximum arm length imbalance of 200 µm, achieving a measured spectral resolution of 13 cm-1 and a free spectral range of 100 cm-1 at wavelengths near 5.5 µm.

Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection.

Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.

Responses of soil N2 O emissions and their abiotic and biotic drivers to altered rainfall regimes and co-occurring wet N deposition in a semi-arid grassland.

Global change factors such as changed rainfall regimes and nitrogen (N) deposition contribute to increases in the emission of the greenhouse gas nitrous oxide (N2 O) from the soil. In previous research, N deposition has often been simulated by using a single or a series of N addition events over the course of a year, but wet N deposition actually co-occurs with rainfall. How soil N2 O emissions respond to altered rainfall amount and frequency, wet N deposition, and their interactions is still not fully understood. We designed a three-factor, fully factorial experiment with factors of rainfall amounts (ambient, -30%) rainfall frequency (ambient, ±50%) and wet N deposition (with/without) co-occurring with rainfall in semi-arid grassland mesocosms, and measured N2 O emissions and their possible biotic and abiotic drivers. Across all treatments, reduced rainfall amount and N deposition increased soil N2 O emissions by 35% and 28%, respectively. A significant interactive effect was observed between rainfall amount and N deposition, and to a lesser extent between rainfall frequency and N deposition. Without N deposition, reduced rainfall amount and altered rainfall frequency indirectly affected soil N2 O emissions by changing the abundance of nirK and soil net N mineralization, and the changes in nirK abundance were indirectly driven by soil N availability rather than directly by soil moisture. With N deposition, both the abundance of nirK and the level of soil water-filled pore space contributed to changes in N2 O emissions in response to altered rainfall regimes, and the changes in the abundance of nirK were indirectly driven by plant N uptake and nitrifier (ammonia-oxidizing bacteria) abundance. Our results imply that unlike wetter grassland ecosystems, reduced precipitation may increase N2 O emissions, and N deposition may only slightly increase N2 O emissions in arid and semi-arid N-limited ecosystems that are dominated by grasses with high soil N uptake capacity.

Silicon photonic on-chip spatial heterodyne Fourier transform spectrometer exploiting the Jacquinot's advantage.

Silicon photonics on-chip spectrometers are finding important applications in medical diagnostics, pollution monitoring, and astrophysics. Spatial heterodyne Fourier transform spectrometers (SHFTSs) provide a particularly interesting architecture with a powerful passive error correction capability and high spectral resolution. Despite having an intrinsically large optical throughput (étendue, also referred to as Jacquinot's advantage), state-of-the-art silicon SHFTSs have not exploited this advantage yet. Here, we propose and experimentally demonstrate for the first time, to the best of our knowledge, an SHFTS implementing a wide-area light collection system simultaneously feeding an array of 16 interferometers, with an input aperture as large as 90µm×60µm formed by a two-way-fed grating coupler. We experimentally demonstrate 85 pm spectral resolution, 600 pm bandwidth, and 13 dB étendue increase, compared with a device with a conventional grating coupler input. The SHFTS was fabricated using 193 nm deep-UV optical lithography and integrates a large-size input aperture with an interferometer array and monolithic Ge photodetectors, in a 4.5mm2 footprint.

Dual-band fiber-chip grating coupler in a 300 mm silicon-on-insulator platform and 193 nm deep-UV lithography.

Surface grating couplers are fundamental building blocks for coupling the light between optical fibers and integrated photonic devices. However, the operational bandwidth of conventional grating couplers is intrinsically limited by their wavelength-dependent radiation angle. The few dual-band grating couplers that have been experimentally demonstrated exhibit low coupling efficiencies and rely on complex fabrication processes. Here we demonstrate for the first time, to the best of our knowledge, the realization of an efficient dual-band grating coupler fabricated using 193 nm deep-ultraviolet lithography for 10 Gbit symmetric passive optical networks. The footprint of the device is 17×10µm2. We measured coupling efficiencies of -4.9 and -5.2dB with a 3-dB bandwidth of 27 and 56 nm at the wavelengths of 1270 and 1577 nm, corresponding to the upstream and downstream channels, respectively.

Design and Simulation Investigation of Si3N4 Photonics Circuits for Wideband On-Chip Optical Gas Sensing around 2 µm Optical Wavelength.

We theoretically explore the potential of Si3N4 on SiO2 waveguide platform toward a wideband spectroscopic detection around the optical wavelength of 2 µm. The design of Si3N4 on SiO2 waveguide architectures consisting of a Si3N4 slot waveguide for a wideband on-chip spectroscopic sensing around 2 µm, and a Si3N4 multi-mode interferometer (MMI)-based coupler for light coupling from classical strip waveguide into the identified Si3N4 slot waveguides over a wide spectral range are investigated. We found that a Si3N4 on SiO2 slot waveguide structure can be designed for using as optical interaction part over a spectral range of interest, and the MMI structure can be used to enable broadband optical coupling from a strip to the slot waveguide for wideband multi-gas on-chip spectroscopic sensing. Reasons for the operating spectral range of the system are discussed.

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations.

Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI-tree species have not been identified. Here, we evaluated how some tree species can control soil nitrification by providing direct evidence of BNI and identifying the nitrifier group(s) affected. First, by comparing 28 year-old monocultures of several tree species, we showed that nitrification rates correlated strongly with the abundance of the nitrite oxidizers Nitrobacter (50- to 1000-fold changes between tree monocultures) and only weakly with the abundance of ammonia oxidizing archaea (AOA). Second, using reciprocal transplantation of soil cores between low and high nitrification stands, we demonstrated that nitrification changed 16 months after transplantation and was correlated with changes in the abundance of Nitrobacter, not AOA. Third, extracts of litter or soil collected from the low nitrification stands of Picea abies and Abies nordmanniana inhibited the growth of Nitrobacter hamburgensis X14. Our results provide for the first time direct evidence of BNI by tree species directly affecting the abundance of Nitrobacter.

Ge-rich graded SiGe waveguides and interferometers from 5 to 11†µm wavelength range.

The mid-infrared (mid-IR) wavelength range hosts unique vibrational and rotational resonances of a broad variety of substances that can be used to unambiguously detect the molecular composition in a non-intrusive way. Mid-IR photonic-integrated circuits (PICs) are thus expected to have a major impact in many applications. Still, new challenges are posed by the large spectral width required to simultaneously identify many substances using the same photonic circuit. Ge-rich graded SiGe waveguides have been proposed as a broadband platform approach for mid-IR PICs. In this work, ultra-broadband waveguides are experimentally demonstrated within unprecedented wavelength range, efficiently guiding light from 5 to 11 µm. Interestingly, losses from 0.5 to 1.2 dB/cm are obtained between 5.1 and 8 µm wavelength, and values below 3 dB/cm are measured from 9.5 to 11.2 µm wavelength. An increase of propagation losses is seen between 8 and 9.5 µm; however, values stay below 4.6 dB/cm in the entire wavelength range. A detailed analysis of propagation losses is reported, supported by secondary ion mass spectrometry measurement, and different contributions are analyzed: silicon substrate absorption, oxygen impurities, free carrier absorption by residual doping, sidewall roughness and multiphonon absorption. Finally, Mach-Zehnder interferometers are characterized, and wideband operation is experimentally obtained from 5.5 to 10.5 µm wavelength.

Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning.

Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above- and belowground plant growth, likely enhancing plant-microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire 'reboots' the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.

Polarization independent and temperature tolerant AWG based on a silicon nitride platform.

A polarization tolerant optical receiver is a key building block for the development of wavelength division multiplexing based high-speed optical data links. However, the design of a polarization independent demultiplexer is not trivial. In this Letter, we report on the realization of a polarization tolerant arrayed waveguide grating (AWG) on a 300-mm silicon nitride (SiN) photonic platform. By introducing a series of individual polarization rotators in the middle of the waveguide array, the polarization dependence of the AWG has been substantially reduced. Insertion losses below 2.2 dB and a crosstalk level better than -29dB has been obtained for transverse electric and transverse magnetic polarizations on a four-channel coarse AWG. The AWG temperature sensitivity has also been evaluated. Thanks to the low thermo-optical coefficient of SiN, a thermal shift below 12 pm/°C has been demonstrated.

Silicon subwavelength modal Bragg grating filters with narrow bandwidth and high optical rejection.

Waveguide Bragg grating filters with narrow bandwidths and high optical rejections are key functions for several advanced silicon photonics circuits. Here, we propose and demonstrate a new, to the best of our knowledge, Bragg grating geometry that provides a narrowband and high rejection response. It combines the advantages of subwavelength and modal engineering. As a proof-of-concept demonstration, we implement the proposed Bragg filters in 220-nm-thick Si technology with a single etch step. We experimentally show flexible control of the filter selectivity, with measured null-to-null bandwidths below 2 nm, and strength of 60 dB rejection with a null-to-null bandwidth of 1.8 nm.

Subwavelength engineering for Brillouin gain optimization in silicon optomechanical waveguides.

Brillouin optomechanics has recently emerged as a promising tool to implement new functionalities in silicon photonics, including high-performance opto-RF processing and nonreciprocal light propagation. One key challenge in this field is to maximize the photon-phonon interaction and the phonon lifetime, simultaneously. Here, we propose a new, to the best of our knowledge, strategy that exploits subwavelength engineering of the photonic and phononic modes in silicon membrane waveguides to maximize the Brillouin gain. By properly designing the dimensions of the subwavelength periodic structuration, we tightly confine near-infrared photons and GHz phonons, minimizing leakage losses and maximizing the Brillouin coupling. Our theoretical analysis predicts a high mechanical quality factor of up to 700 and a remarkable Brillouin gain yielding 3500(W⋅m)-1 for minimum feature size of 50 nm, compatible with electron-beam lithography. We believe that the proposed waveguide with subwavelength nanostructure holds great potential for the engineering of Brillouin optomechanical interactions in silicon.

Sub-decibel silicon grating couplers based on L-shaped waveguides and engineered subwavelength metamaterials.

The availability of low-loss optical interfaces to couple light between standard optical fibers and high-index-contrast silicon waveguides is essential for the development of chip-integrated nanophotonics. Input and output couplers based on diffraction gratings are attractive coupling solutions. Advanced grating coupler designs, with Bragg or metal mirror underneath, low- and high-index overlays, and multi-level or multi-layer layouts, have proven less useful due to customized or complex fabrication, however. In this work, we propose a rather simpler in design of efficient off-chip fiber couplers that provide a simulated efficiency up to 95% (-0.25 dB) at a wavelength of 1.55 µm. These grating couplers are formed with an L-shaped waveguide profile and synthesized subwavelength grating metamaterials. This concept jointly provides sufficient degrees of freedom to simultaneously control the grating directionality and out-radiated field profile of the grating mode. The proposed chip-to-fiber couplers promote robust sub-decibel coupling of light, yet contain device dimensions (> 120 nm) compatible with standard lithographic technologies presently available in silicon nanophotonic foundries. Fabrication imperfections are also investigated. Dimensional offsets of ± 15 nm in shallow-etch depth and ± 10 nm in linewidth's and mask misalignments are tolerated for a 1-dB loss penalty. The proposed concept is meant to be universal, which is an essential prerequisite for developing reliable and low-cost optical couplers. We foresee that the work on L-shaped grating couplers with sub-decibel coupling efficiencies could also be a valuable direction for silicon chip interfacing in integrated nanophotonics.

Engineering third-order optical nonlinearities in hybrid chalcogenide-on-silicon platform.

We demonstrated a class of highly nonlinear hybrid waveguide structures based on infiltration of As2S3 chalcogenide glass into silicon slot waveguides. The nonlinear properties of the hybrid waveguides were precisely quantified via a bidirectional top-hat D-scan method, enabling a direct comparison between properties measured using different device geometries. We experimentally demonstrate hybrid As2S3-Si slot waveguides with a two-photon absorption (TPA) figure of merit exceeding 2 at near infrared wavelengths. These waveguides largely satisfy the critical criterion for efficient nonlinear integrated photonics (FOMTPAwg>1), allowing phase shifts greater than π with minimal overall losses. These results pave the way for efficient and robust ultrafast all-optical devices and circuits in large-scale silicon photonics technology.