Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere

The rhizosphere is the interface between plant roots and soil where intense, varied interactions between plants and microbes influence plants' health and growth through their influence on biochemical cycles, such as the carbon, nitrogen, and iron cycles. The rhizosphere is also a changing environment where oxygen can be rapidly limited and anaerobic zones can be established. Microorganisms successfully colonize the rhizosphere when they possess specific traits referred to as rhizosphere competence. Anaerobic respiration flexibility contributes to the rhizosphere competence of microbes. Indeed, a wide range of compounds that are available in the rhizosphere can serve as alternative terminal electron acceptors during anaerobic respiration such as nitrates, iron, carbon compounds, sulfur, metalloids, and radionuclides. In the presence of multiple terminal electron acceptors in a complex environment such as the rhizosphere and in the absence of O2, microorganisms will first use the most energetic option to sustain growth. Anaerobic respiration has been deeply studied, and the genes involved in anaerobic respiration have been identified. However, aqueous environment and paddy soils are the most studied environments for anaerobic respiration, even if we provide evidence in this review that anaerobic respiration also occurs in the plant rhizosphere. Indeed, we provide evidence by performing a BLAST analysis on metatranscriptomic data that genes involved in iron, sulfur, arsenate and selenate anaerobic respiration are expressed in the rhizosphere, underscoring that the rhizosphere environment is suitable for the establishment of anaerobic respiration. We thus focus this review on current research concerning the different types of anaerobic respiration that occur in the rhizosphere. We also discuss the flexibility of anaerobic respiration as a fundamental trait for the microbial colonization of roots, environmental and ecological adaptation, persistence and bioremediation in the rhizosphere. Anaerobic respiration appears to be a key process for the functioning of an ecosystem and interactions between plants and microbes

In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes

International audienceThe essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome of Xanthomonas hortorum pv. vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativa L.) which belongs to the plant-pathogen reservoir genus Xanthomonas and is affiliated to the family Xanthomonadaceae. No practical means of disease control or preventionagainst this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome of X. hortorum pv. vitians LM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features of Xanthomonas or Xanthomonadaceae species, or acquired through horizontal genetransfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study of X. hortorum pv. vitians

Retrieval of fire plume heights from IR satellite measurements

Large fire events are known to inject important amounts of pollutants into the atmosphere. Those pollutants are concentrated in plumes and can be transported far from the fire source, especially when the injection is directly into the free troposphere. The knowledge of fire injection height, which is important for atmospheric chemistry models and dispersion models, is often inaccurate. In this work we explore the possibility to obtain information about the altitude of fire plumes, using IASI radiances, and in particular the information they carry on the carbon monoxide (CO) vertical profile and the ethylene (C2H4) total column. For CO it is well known that IASI allows retrieving a weakly resolved profile in most situations with, in the best cases, about two independent pieces of information. The retrieval of CO profiles is achieved operationally and globally with the FORLI software, which relies on the Optimal Estimation method. The use in FORLI of an a priori profile representative of background conditions, and of an associated covariance matrix with significant correlation between vertical levels, results in generally smoothed retrieved CO profiles, without a pronounced maximum. We will show that the use of an alternative choice of a priori constrain (with less correlation) allows capturing local enhancements in CO over a narrow range of altitudes, which can then be assigned to a plume altitude. A series of well-documented fire events, with varying injection heights, will be discussed to evaluate the reliability of the method; the validation will be performed mainly with measurements from CALIPSO. In addition to CO, we will show that C2H4 measurements from IASI can be used as a robust indicator of fire plumes injected above the boundary layer. This is based on the fact that the sensitivity of IASI to boundary layer C2H4 is generally too low to produce a detectable signal in the radiances, while the opposite prevails when C2H4 is found at higher altitude. The availability of a decadal set of C2H4 from IASI allows to verify this on a very large set of situations. We will discuss the results mainly by correlating the C2H4 columns from IASI to injection heights from the Global Fire Assimilation System (GFAS), which operationally assimilates Fire Radiative Power from different satellite sensors.info:eu-repo/semantics/nonPublishe

Effects of the denitrification inhibitor “procyanidins” on the diversity, interactions, and potential functions of rhizosphere-associated microbiome

International audienceSome plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil

Large VOC enhancements in recent massive wildfires observed from space

International audienceMassive wildfires erupted in Amazonia and through the subarctic region in summer 2019, and in Australia in winter 2019-2020. During such biomass burning events, sizeable amounts of volatile organic compounds (VOCs) can be emitted directly by the fires as well as rapidly produced in plumes via the degradation of short-lived gas precursors. The VOCs have a significant impact on tropospheric chemistry by, e.g., affecting the oxidative capacity of the atmosphere. Nadir-viewing infrared sensors onboard meteorological satellites provide global and spatially dense observations that are very useful to track biomass burning events throughout the globe and to provide trace gas quantification in fire plumes.We apply a general retrieval framework, based on an artificial neural network, to derive the integrated abundance (total column) of several major VOCs from the infrared radiance spectra recorded by IASI (Infrared Atmospheric Sounding Interferometer) embarked on the Metop platforms. Quasi-global distributions of methanol (CH3OH), formic (HCOOH) and acetic (CH3COOH) acids, PAN, acetone (CH3COCH3), acetylene (C2H2) and hydrogen cyanide (HCN) column abundance are produced twice-daily from the a.m. and p.m. overpasses of the satellite instrument. In particular, we use the IASI data to produce daily regional snapshots over biomass burning areas of interest and to quantify the VOC enhancements in the plumes from the recent Amazonian, Australian and subarctic wildfires. Finally, the abundance ratios of these VO

Jet-cooled ethylene cavity ring-down spectroscopy between 5880 and 6200 cm−1

International audienceAbsorption spectra of jet-cooled ethylene (ethene, C2H4) are recorded at three different rotational temperatures (6/8 K, 12 K, 38 K) using cavity ring-down spectroscopy (CRDS) in the 5880-6200 cm−1 spectral region. Rotational cooling is used to determine the various vibrational band centers by simplifying drastically the rotational band structure. A line-by-line assignment, based on a direct comparison with the TheoReTS variational line list and a systematic use of lower state combination difference (LSCD), is performed. Experimental line lists including line position and line integrated absorption cross sections are drawn up. The 6/8 K, 12 K and 38 K spectra contain 668, 1553 and 1679 absorption lines respectively. Overall, 320 rovibrational lines are assigned across 20 interacting vibrational bands. Among the 20 vibrational cold bands identified in this work, 14 had never been observed before. Line intensities are in the range of 10−24 - 10−20 cm/molecule. A direct comparison between our work and the TheoReTS and ExoMol theoretical line lists, as well as with the recent experimental work of Ben Fathallah et al. 2024 is provided

Spectroscopy of hydrocarbons relevant to the atmospheres of hot Jupiter exoplanets in the 1.6-1.7 μm range: unambiguous assignment of ethylene transitions

International audienceAccurate knowledge of the absorption fingerprint of the species expected in the atmospheres of the hot Jupiter exoplanets is required to allow their detection. Methaneᵃ and acetyleneᵇ were already detected in such environments, and the presence of other small hydrocarbons such as ethylene (C₂H₄) is expected. However, spectral assignment of C₂H₄ transitions is not available at wavenumbers higher than 3500 cm⁻¹, partly due to its highly congested absorption spectrum at room temperature. To provide accurate assignments of the cold transitions, we perform cavity ring-down spectroscopy of a jet-cooled ethylene gas sample in the 1.6-1.7 µm spectral range. The gas contained in a high-pressure reservoir is expanded into a low-pressure chamber through an 8.5cm-long slit with a tunable opening width ranging from 0 to 350 µm. This process induces a simplification of the absorption spectrum by reducing drastically the rotational temperature and by narrowing the absorption line widths. Three spectra were recorded with a vibrational temperature of about 220K but different rotational temperatures: 5K, 35K, and 75K. Unambiguous assignment of the observed lines is performed using the TheoReTS ab initio line listᶜ and the temperature dependence of the transition intensities

Agrobacterium fabrum C58 involved nitrate reductase NapA and antisense RNA NorR to denitrify

International audienceABSTRACT Agrobacterium fabrum C58 is a plant-associated bacterium that is able to denitrify under anoxic conditions. The cluster of denitrification genes harbored by this strain has been well characterized. It includes nir and nor operons encoding nitrite and nitric oxide reductases, respectively. However, the reductase involved in nitrate reduction has not yet been studied and little information is available on denitrification regulators in A. fabrum C58. In this study, we aimed to (i) characterize the nitrate reductase, (ii) determine its role in A. fabrum C58 fitness and root colonization and (ii) reveal the contribution of small RNA on denitrification regulation. By constructing a mutant strain defective for napA, we demonstrated that the reduction of nitrate to nitrite was catalyzed by the periplasmic nitrate reductase, NapA. We evidenced a positive role of NapA in A. fabrum C58 fitness and suggested that A. fabrum C58 is able to use components exuded by plant roots to respire anaerobically. Here, we showed that NorR small RNA increased the level of norCBQ mRNA and a decrease of NorR is correlated with a decrease in N2O emission. Together, our results underscore the importance of understanding the denitrification pathway at the strain level in order to develop strategies to mitigate N2O production at the microbial community level

Unambiguous assignment of ethylene transitions in the 5900-6200 cm-1 range

Among other species, methane [1] and acetylene [2] were detected in the atmospheres of Hot Jupiter exoplanets. The James Webb Space Telescope is expected to detect other small hydrocarbons including ethylene (C2H4), in particular in the near-infrared spectral range [3]. High-temperature and high-resolution laboratory data are therefore needed both to unambiguously detect this species and to retrieve its atmospheric concentration and temperature profiles. Our aim is to produce high-temperature spectroscopic data of ethylene in the 1.6-1.7 μm spectral region using our SMAUG hypersonic wind tunnel, which has already been applied to methane [4,5]. Nevertheless, due to the very dense absorption spectrum of ethylene even at room temperature, a preliminary measurement campaign was carried out at very low temperatures under slit jet-cooled conditions to first provide accurate assignments of cold band transitions. A series of three spectra were recorded by cavity ringdown spectroscopy and tunable distributed feedback laser diodes at rotational temperatures of 6K, 16K and 54K using either Ar/C2H4 or N2/C2H4 gas mixtures. Unambiguous assignment of the observed rovibrational lines is performed using the TheoReTS ab initio line list [6] and the SPVIEW/XTDS software package [7]. These transitions have been attributed to seven interacting vibrational bands: v2 +v3 +v11, v2 +v6 +v9, v1 +v11, v5 +v11, v1 +v2 +v12, v5 + v9, and v9 + 2v12.[1] M. Swain, G. Vasisht, G. Tinetti, Nature, 452, 329{331 (2008).[2] P. Giacobbe et al., Nature, 592, 205{208 (2021).[3] D. Gasman,et al., A&A, 659, A114 (2022).[4] E. Dudás et al., J. Chem. Phys., 152, 134201 (2020).[5] E. Dudás et al., Icarus, 394, 115421 (2023).[6] M. Rey, et al., J. Mol. Spectrosc., 327, 138{158 (2016)[7] Ch. Wenger, et al., J. Mol. Spectrosc., 251, 102-113 (2008