Ugo Jacovella
email: ugo.jacovella@universite-paris-saclay.fr

Branko Ruscic

Ning L Chen

Hai-Linh Linh Le

Séverine Boyé-Péronne

Madhusree Sebastian Hartweg

Roy Chowdhury

Gustavo Adolfo Garcia

Jean-Christophe Loison

Bérenger Gans
email: berenger.gans@universite-paris-saclay.fr

Se- Bastian Hartweg

Madhusree Roy Chowdhury

Refining thermochemical properties

come

Refining thermochemical properties of CF, SiF, and their cations by combining photoelectron spectroscopy, quantum chemical calculations, and the Active Thermochemical Tables approach

Introduction

The first group 14 monofluoride radicals, namely fluoromethylidyne (CF) and fluorosilylidyne (SiF), along with their cations fluoromethyliumylidene (CF + ) and fluorosilyliumylidene (SiF + ), are commonly found in plasmas employed for the purpose of silicon-containing semiconductor material surface etching. [1][2][3] In addition to being one of the most abundant ions present in semiconductor processing, 3 CF + has been detected in diverse regions of outer space. [4][5][6][7] It has thus been identified as a key intermediate in the chemistry of fluorine-bearing molecules in diffuse and dense interstellar gas clouds. 8,9 Although the astronomical detection of SiF and SiF + is still awaiting, their presence in outer space as well as their role in the chemistry of silicon in gas phase and on grains is strongly suspected. Indeed, reactions involving SiF + are already incorporated in astrochemical models. 8 Thermodynamic properties such as enthalpies of formation, dissociation energies, and adiabatic ionisation energies are of upmost importance for refining chemical models of fluorinated chemistry in plasmas and in space. Furthermore, accurate thermodynamic properties are very well suited to benchmarking the accuracy of existing and upcoming state-of-the-art quantum chemical calculations, particularly with respect to pushing the limits of the long-standing challenge of obtaining accurate thermochemical data for fluorinated compounds. [10][11][12][13][14] Dyke and coworkers have published two papers presenting the He I photoelectron spectra of CF 15,16 from which they determined the adiabatic ionisation energies of the X + 1 S + X 2 P and a + 3 P X 2 P ionising transitions of CF to be 9.11 ± 0.02 eV and 13.94 ± 0.02 eV, respectively. From photoelectron spectra, the w + e value of CF + was derived initially to be 1840 ± 30 cm 1 , 15 and later revised to 1810 ± 30 cm 1 . 16 The CF + cation has also been investigated using direct infrared (IR) diode laser spectroscopy. 17,18 Preliminary work from Hirota and coworkers 17 has yielded precise structural information on CF + from its vibronic ground state (r + e = 1.154272(35) Å). Subsequently, Saykally and coworkers 18 have extended the IR study of CF + to the seven lowest vibrational levels of the electronic ground state, providing precise vibrational constants such as w + e = 1792.6654(18) cm 1 and w e x + e = 13.229668(54) cm 1 , as well as r + e = 1.1542551(25) Å, the latter being in good agreement with Hirota et al. However, of the two photoelectron spectroscopic studies, only the most recent one 16 reported a vibrational frequency (1810 ± 30 cm 1 ) congruent with the accurate constants of Saykally and coworkers. 18 The spectroscopic molecular constants are also well predicted by multireference configuration interaction (MRCI) calculations for the lowest singlet and triplet electronic states of CF + . 19 Subsequently, the landscape of the CF + electronic states has been further explored along with several Rydberg states. 20,21 The dissociation energy of CF + ground state has been estimated 16 as D 0 (CF + ) = 7.82 ± 0.12 eV, based on combining the ionisation energies of CF and carbon atom with the dissociation energy of CF of 5.67 ± 0.10 eV from electron-ionisation mass spectrometric studies. 22 This is just within the combined error bars compared to the value obtained in the work of Saykally, 18 D 0 (CF + ) = 7.698 ± 0.004 eV, extracted from the fit based on a crude Morse potential model. Theodorakopoulos and coworkers 20 calculated the dissociation energy of CF + using MRCI and obtained a significantly underestimated value (D 0 (CF + ) = 6.73 eV) compared to those extracted from experimental studies. Later, Letelier and coworkers [START_REF] Inostroza | Spectrochim[END_REF] made the first step toward a reconciliation of the experimental results with theory by using MRCI+Q/aug-cc-pV5Z calculations. They obtained a D 0 value of 7.54 eV.

There is a remarkable paucity of photoelectron spectroscopic data available for SiF. No direct measurement of the adiabatic ionisation energy of SiF has been obtained, and the indirectly derived values span a rather large energy range. Using ion chemistry, one can estimate 7.54 ± 0.16 eV 24 and 7.08 ± 0.10 eV, 25 whereas extrapolation from Rydberg spectroscopy leads to 7.26 eV, 26 7.31 eV, 27 and 7.31 ± 0.02 eV. 28 The two calculations of the adiabatic ionisation energy available in the literature report 7.36 eV at the coupled cluster single, double, and pertubative triple level and complete basis set extrapolation (CCSD(T)/CBS) 29 and 7.41 eV at the G3(CC)/B2df+ level, 30 although neither of the two is sufficiently accurate to confidently provide a value within chemical accuracy (with uncertainty less than ± 1 kcal.mol 1 or ± 0.04 eV). However, the SiF + structural information and vibrational properties in the electronic ground state have been precisely determined using microwave (r + e = 1.5264950(2) Å; w + e = 1050.7(2) cm 1 ) 31 and IR spectroscopy (r + e = 1.5265(8) Å; w + e = 1050.3757(13) cm 1 ; w e x + e = 4.9462(4) cm 1 ). 32 Several values for the SiF + dissociation energy have been extracted from experimental studies D 0 (SiF + ) = 6.3 eV, 33 6.46 ± 0.14 eV, 34 6.32 ± 0.11 eV, 24 all of which are lower than the most accurate theoretical values obtained either using CCSD(T) with CBS extrapolation, 35 D 0 = 6.92 ± 0.04 eV, configuration-interaction method, 36 D 0 = 6.60 eV, or MP4SDTQ, 19 D 0 = 6.85 eV. It is worth noting that, while highlevel calculations appear to underestimate the experimentally derived dissociation energy of CF + , they seem to overestimate that of SiF + . This paper presents the threshold photoelectron and photoion yield spectra of SiF and CF radicals in the vicinity of their first ionisation threshold. The spectra are analysed with the support of ab initio calculations that aid the extraction of relevant spectroscopic parameters. The new experimental values were added to the thermochemical network underlying the Active Thermochemical Ta-bles (ATcT) approach, [37][38][START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] thus producing further improved thermochemical parameters of SiF, CF and the corresponding cations.

Methodologies

Experimental details

The experiments were performed at the SOLEIL synchrotron facility, on the DESIRS beamline. [START_REF] Nahon | [END_REF] The experimental setup combining the DELICIOUS3 spectrometer 41,42 and the flow-tube reactor has been described elsewhere. 43,44 The experimental spectra recorded for CF and SiF have been obtained using the conditions described in Refs. 45 and 46, respectively, in which CF and SiF were side products of the reaction of F with CH 4 (or C 2 H 4 ) or SiH 4 , respectively. The output of the flow-tube reactor was sampled through two consecutive skimmers before reaching the interaction region at the centre of DE-LICIOUS3. From CF + and SiF + photoion images, mean velocities were measured along the molecular beam at 915 and 1010 m/s, corresponding to translational temperatures in the 200-220 K range.

In the present paper, only details concerning the resolutions of the presented spectra are summarised. The spectral resolutions of the ion yields are 0.72 Å (5.8 meV at 10 eV) for CF and 2.16 Å (17.4 meV at 10 eV) for SiF, which correspond to the photon spectral resolution. The final spectral resolutions d E of the slow photoelectron spectra (SPES) are estimated to be 14 meV at 9.5 eV and 24 meV at 7.5 eV for the CF and SiF spectra, respectively. The energy scale has been calibrated using the He third order and Si atomic transitions, with an energy scale uncertainty of ±3 meV for CF and ±6 meV for SiF, respectively. Note that the extraction field (F) used to extract the ions and the electrons (88.7 V/cm) leads to a field-induced downshift of the ionisation energies of approximately 7 meV, following the well-established formula 6 p F (in cm 1 with F in V/cm). 47 Although the universality of the Stark shift in polyatomic systems has been previously questioned, 48,49 we have checked in our experiment using absorption lines from the gas filter (not subject to the Stark shift) and known adiabatic ionisation energies of molecules that the above-mentioned Stark shift applied within the error bars.

Calculation details

Supporting ab initio calculations on the electronic states of CF, CF + , SiF, and SiF + were carried out using the internally contracted multireference configuration interaction method with Davidson correction (icMRCI+Q) with complete active space selfconsistent field (CASSCF) wave-functions. The CASSCF and MRCI calculations were performed at full valence, i.e., 11 electrons for CF and SiF (10 for CF + and SiF + ). These electrons were distributed in 8 orbitals keeping the 1s orbital of carbon and fluorine atom and the 1s, 2s, and 2p orbitals of silicon atom doubly occupied. All calculations were performed using the MOL-PRO 2016 package. [START_REF] Werner | version 2016, a package of ab initio programs[END_REF] Single point calculations were performed at the aug-cc-pVnZ (n = T, Q, 5, and 6) basis set [START_REF] Kendall | [END_REF] for the equilibrium geometries and anharmonic frequencies (using the DI-ATOMIC routine in MOLPRO where the potential curves were fit-ted with a polynomial of 8 th order) allowing the spectroscopic constants to be calculated (w e , w e x e , and w e y e ) for the CF(X 2 P), CF + (X + 1 S + ), SiF(X 2 P) and SiF + (X + 1 S + ) states. CBS extrapolations were carried out using the aug-cc-pVnZ (n = T, Q, 5, and 6) basis set series. The CASSCF and dynamical correlation (E MRCI+Q E CASSCF ) energies were extrapolated using the E CASSCF (CBS)+A⇥exp( Bn) and E Corr (CBS)+C ⇥n 3 functions, respectively. The calculated energies reported in this paper correspond to E CASSCF (CBS) + E corr (CBS). The anharmonic constants (w e x e and w e y e ) could not be confidently extrapolated to CBS because of their weak dependence on the basis used; instead, the values obtained with the largest basis set (aug-cc-pV6Z) were used. Our calculated values are reported in Tables 1 and2 and discussed in the following section.

Results

The first ionising transitions of CF and SiF arise from one-electron removal from the 2p orbital, which is the first anti-bonding (p ⇤ ) orbital. This leads to a X + 1 S + X 2 P r photoionising transition. Looking at the molecular orbital diagrams, one can assume that the ionisation process removes mainly one of the unpaired p-electrons on C ( 3 P) and Si ( 3 P) atoms for CF and SiF, respectively. In the analogous cases of SiH and CH, the p orbitals are rather weakly perturbed, as witnessed by the modest difference in the ionisation energies (IEs) of Si (8.15166 ± 0.00003 eV) 52 and SiH (7.934 ± 0.005 eV), 46 or those of C (11.260288 ± 0.000002 eV) 53 and CH (10.640 ± 0.004 eV). 54 In CF and SiF radicals, the interactions between the p-orbitals of C/Si atoms and the doubly occupied p-orbital of the fluorine atom are greater, which leads to a more pronounced decrease of IEs for CF (9.128 ± 0.006 eV) and SiF (7.381 ± 0.009 eV).

Photoelectron and photoion yield spectra of CF

In Fig. 1, the mass-selected ion yield of CF is depicted on top of the photoelectron signal (PES) matrix, i.e. the coincidence signal of the electrons (resolved by kinetic energy) as a function of photon energy. The vertical lines (resonant with photon energy) observed above 11 eV correspond to autoionisation of neutral CF Rydberg states converging to several vibronic states of CF + .

In Fig. 2, the corresponding CF threshold photoelectron spectrum is displayed in black and compared with our harmonic Franck-Condon (FC) simulation in red. The experimental spectrum exhibits a progression up to v + = 6, as well as one hot band around 9 eV arising from the v + = 0 v = 1 transition. While the agreement is satisfactory at low energy, the calculated spectrum starts to progressively deviate from the experimental spectrum above 9.75 eV due to the absence of the anharmonic component in the simulation. Based on the vibrational FC simulation, the origin band is unambiguously assigned. From the prominent vibrational progression, one can extract the harmonic frequency w + e and the corresponding anharmonic constant w e x + e . Fig. 3 shows a plot of the observed peak apexes as a function of (v + + 1 2 ). The obtained data set was fitted using a second-order polynomial expression. Note that, owing to the aforementioned autoionisation processes, the transition to v + = 11 was observed, from which the quality of the fit and thus of evaluation of the anharmonicity was greatly improved. Indeed, autoionisation resonances allow sampling of the molecular potential beyond the Franck-Condon region that is not accessible by one-photon direct ionisation. 55 The fitted spectroscopic constants are w + e = 1786.5 ± 5.5 cm 1 and w e x + e = 11.89 ± 0.44 cm 1 , in reasonable agreement with the very accurate constants obtained by Saykally 18 , as well as with the frequency of 1810 ± 30 cm 1 reported by Dyke et al. 16 (see Table 1).

The apex position of the origin band in Fig. 2 can be determined as 9.121 eV, which, after a correction for the Stark shift, becomes 9.128 ± 0.004 eV. It is important to note here that the adiabatic ionisation energy, which is a thermodynamically-relevant quantity, by definition corresponds to the energy difference between the lowest actually existing rovibronic level of the neutral and that of the ion. 56 (Mutatis mutandis, the same is true for all thermodynamically-relevant quantities, such as dissociation energies and other reaction energies at 0 K. 56 ) Thus, in CF the adiabatic ionisation energy corresponds to the

X + 1 S + (v + = 0, J + = 0) X 2 P 1/2 (v = 0, J = 1/2) transition.
In regular photoelectron spectroscopy, when individual rotational transitions are not resolved, the standard practice is to report the apex of the vibrational peak that was identified as the v + = 0 v = 0 transition as the adiabatic ionisation energy. This tacitly implies the assumption that the underlying rotational envelope is not shaded either to the red or to the blue, i.e. that the Q branch is rather compact and that the lateral branches (P and R, as well as higher branches, such as O and S, if they happen to be allowed) are symmetric, which may or may not be correct.

However, the nature of the ground state of neutral CF introduces an additional complication. Namely, X 2 P r undergoes spinorbit coupling (as quantified by the corresponding coupling constant [START_REF] Huber | Molecular Spectra and Molecular Structure. IV. Constants of Diatomic Molecules[END_REF][START_REF] Porter | [END_REF] A 0 = 77.11 ± 0.01 cm 1 ), with 2 P 1/2 as the lower and 2 P 3/2 as the higher component. Consequently, the v + = 0 v = 0 spectral peak in Fig. 2 almost certainly contains an unresolved hot band originating from the upper 2 P 3/2 component of the neutral. vibrational energy / eV

(v + + 1 2
)

ω e + = 1786.5 ± 5.5 cm -1 ω e x e + = 11.89 ± 0.44 cm -1

Fig. 3 Energies of the lowest vibrational levels of the electronic ground state of CF + with respect to its v + = 0 level as a function of (v + + 1 2 ). The red crosses represent our harmonic calculations and the black circles our measurements. The blue line corresponds to a second-order polynomial fit of our experimental values. See text for details.

Prima facie, one would expect that the presence of such an unresolved hot band will cause a shift of the apparent apex to the red, the amount of which depends, inter alia, on the thermal population of the additional component.

To that end, an approximate simulation of the rotational envelope has been performed to estimate the potential shift of the peak apex relative to the adiabatic ionisation energy. While the energy terms of 1 S + rotational levels are straightforward, the rotational levels of the 2 P state were calculated using the Hamiltonian that correctly describes the coupling of the spin with the orbital and the rotational angular momenta, as appropriate for partial spin uncoupling pertinent to a transition from Hund's case (a) to case (b), 59,[START_REF] Herzberg | Molecular Spectra and Molecular Structure. I. Spectra of Diatomic Molecules[END_REF] following the elegantly re-derived formulation by Hougen. [START_REF] Hougen | The calculation of rotational energy levels and rotational line intensities in diatomic molecules[END_REF] The spectroscopic constants of CF and CF + were taken from Refs. 58 and 17, respectively. With these, the Hamiltonian for the X 2 P r state of CF produces the term values of F 1 = -37.15 cm 1 for 2 P 1/2 , J = 1/2 and F 2 = 41.46 cm 1 for 2 P 3/2 , J = 3/2. Notably, the lowest rotational levels of each of the two spin-orbit components of 2 P r of CF appear to be almost symmetrically split by roughly ± A 0 /2 below and above the reference level (vibrationless/rotationless energy level before any spin-orbit consideration). This is in rather stark contrast to the recently discussed situation of spin-orbit-rotation coupling in the otherwise analogous case of X 2 P r of CH, [START_REF] Thorpe | [END_REF] where both F 1 = 0.15 cm 1 and F 2 = 17.97 cm 1 are positive quantities, or, for that matter, to the quite asymmetric splitting in the well-known case of X 2 P i of OH, [63][64][65] neither of which conforms to a symmetric ± A 0 /2 splitting of the spin-orbit components that is frequently presumed in theoretical calculations.

For the spectral simulation of the rotational envelope, the ro- tational temperature of 200 K was used as it corresponds to the translational temperature of the beam at the output of the flowtube reactor (see the "Experimental details" subsection). The simulated envelope strongly suggests that the adiabatic ionisation energy (X + 1 S + (v + = 0, J + = 0) X 2 P 1/2 (v = 0, J = 1/2)) is, in fact, quite close to the actual maximum of the observed band, primarily because of two opposing tendencies: the unresolved hot band originating from X 2 P 3/2 indeed tends to shift the apex of the experimental peak slightly toward the red, but this is nearly entirely counteracted by the shading toward the blue of the rotational envelope belonging to transitions that originate from X 2 P 1/2 .

After the field-induced Stark-shift correction of 7 meV and an estimation of the uncertainty from our rotational contour simulation, the resulting adiabatic ionisation energy is IE ad (CF) = 9.128 ± 0.006 eV. This can be compared to the value of 9.120 ± 0.005 eV obtained from the publicly available version of ATcT (ver. 1.124) [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] . A variance decomposition analysis of the provenance 66 indicates that the two top contributors to the ATcT value are the experimental ionisation energy of 9.11 ± 0.01 eV determined by Dyke et al. 15 and the difference between the adiabatic ionisation energies of CF 3 and CF of 0.055 ± 0.03 eV determined by Asher and Ruscic. 67 Of note is also that our calculated adiabatic ionisation energy, 9.059 eV (see Table 2), slightly underestimates the experimental value (by 0.07 eV), but is otherwise in quite reasonable agreement with the experiment, particularly if one considers that the species in question is fluorinated.

Photoelectron and photoion yield spectra of SiF

Similarly as for CF, Fig. 4 represents the mass-selected ion yield of SiF superimposed on the PES matrix, where autoionisation features are observed. Fig. 5 displays the threshold photoelectron spectrum (black trace) and its harmonic FC simulation (red trace). The spectrum consists of one hot band, a progression in SiF vibration from the origin band to v + = 3, followed at higher energy by a long high v + series from 20 to 25 caused by resonant autoionisation processes. From our ab initio calculations, we checked that no other electronic states of SiF + were located in this energy region. Indeed, the first triplet ( 3 P) and singlet ( 1 S + ) states are located around 11.83 eV and 13.71 eV above the neutral ground state, respectively. The harmonic FC calcu- lation reproduces satisfactorily the experimental spectrum. The observed energies in the vibrational progression are plotted as a function of (v + + 1 2 ) in Fig. 6. The blue line results from a second-order polynomial fit, leading to w + e = 1056.8 ± 5.2 cm 1 and w e x + e = 5.17 ± 0.20 cm 1 in good agreement with the literature values, see Table 1. As in the case of CF, the inclusion of high v + states accessible via autoionisation processes significantly improves the obtained fit.

From our measurement displayed in Fig. 5, we can extract the band maximum of the origin band of the SiF photolectron spectrum to be 7.372 ± 0.007 eV. Similarly to the case of CF, the rotational envelope was estimated using the spectroscopic constants for SiF and SiF + from Refs. 68 and 31, respectively. Once again, it was found that the adiabatic ionisation energy (X + 1 S + (v + = 0, J + = 0) X 2 P 1/2 (v = 0, J = 1/2)) is very close to the band maximum, for essentially the same reasons as in the case of CF.

The adiabatic ionisation energy is obtained after correcting for field-induced Stark shift (+7 meV) and estimating the uncertainty in the position of the apex of the vibrational peak from our rotational contour simulation. The corresponding final value of the adiabatic ionisation energy IE ad (SiF) = 7.379 ± 0.009 eV. Again, our calculated adiabatic ionisation energy, 7.337 eV (see Table 2), slightly underestimates the experimental value (by 0.04 eV), but is otherwise in reasonable agreement.

Thermochemical considerations

The usual approach to developing new or improved thermodynamic quantities in studies like the present one is to use traditional sequential thermochemistry (A begets B, B begets C, etc.). For instance, since the adiabatic ionisation energy defines the thermodynamic difference between the 0 K enthalpies of formation of the cation and the neutral, the presently determined IE ad (CF) = 9.128 ± 0.006 eV can be combined with the 0 K enthalpy of formation of CF, such as that currently available from ATcT, [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] ω e + = 1056.8 ± 5.2 cm -1 ω e x e + = 5.17 ± 0.20 cm -1

Fig. 6 Energies of the lowest vibrational levels of the electronic ground state of SiF + with respect to its v + = 0 level as a function of (v + + 1 2 ). The red crosses represent our harmonic calculations and the black circles our measurements. The blue line corresponds to a second-order polynomial fit of our experimental values.

rive D f H 0 (CF + ) = D f H 0 (CF) + IE ad (CF) = 268.60 ± 0.14 kcal/mol (which can be in turn compared to the 0 K value for the ion of 268.42 ± 0.11 kcal/mol available directly from ATcT; [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] notably, the corresponding IE ad (CF), as reported by ATcT, is 9.116 ± 0.005 eV, the difference from the current experiment being just about contained -within a round-off error -by the combined uncertainties). After setting the 0 K enthalpies of formation, the corresponding 298.15 K values can be derived as D f H 298 (CF) = 58.968 ± 0.029 kcal/mol and D f H 298 (CF + ) = 269.37 ± 0.14 kcal/mol (the latter within the stationary electron convention 56 ) with the aid of the 298.15 K enthalpy increments of CF (2.167 kcal/mol), [START_REF] Gurvich | Thermodynamic Properties of Individual Substances[END_REF] CF + (2.074 kcal/mol), [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] graphite (0.251 kcal/mol), [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] and F 2 (2.109 kcal/mol). [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] Going further with the sequential thermochemistry approach, one can take the 0 K dissociation energy of CF, D 0 (CF) = 5.654 ± 0.002 eV from ATcT [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] and combine it with the currently determined IE ad (CF) and the accurately known IE(C) 53 to obtain D 0 (CF + ) = D 0 (CF) + IE(C) IE ad (CF) = 7.786 ± 0.007 eV (which can again be compared to the publicly available ATcT value of 7.794 ± 0.005 eV). [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] The corresponding 298.15 K bond dissociation enthalpies are BDE 298 (CF) = 5.695 ± 0.002 eV and BDE 298 (CF + ) = 7.833 ± 0.007 eV (after utilising the aforementioned enthalpy increments for CF and CF + together with those of the C atom, C + ion, and F atom, 1.562, 1.589, and 1.558 kcal/mol, respectively). [START_REF] Gurvich | Thermodynamic Properties of Individual Substances[END_REF] However, the derivations delineated above are entirely dependent not only on the accuracy of the newly determined IE ad (CF), but also on the tacit assumption that auxiliary thermochemical quantities, in this case D f H 0 (CF) and D 0 (CF), have been a priori firmly established, and that thus the new IE ad (CF) leads simply to a revision of D f H 0 (CF + ) and D 0 (CF + ). In this particular case the putative robustness of the available values for D f H 0 (CF) and D 0 (CF) does not appear unreasonable, given that the provenances of the ATcT values include, inter alia, state-of-the-art electronic structure computations capable of sub-kJ/mol accuracies, such as several flavors of W4, [START_REF] Karton | [END_REF][72][73][74] HEAT, 65,75 and FPD, 76 all of which appear mutually entirely consistent.

Nonetheless, in a general case the assumptive premise of robustness of the auxiliary thermochemistry may or may not be warranted. In fact, the new measurement may very well also imply the need for revisions or adjustments of the auxiliary thermochemistry. One of the additional potential problems of sequential thermochemistry is that while it tends to produce an improvement in the derived thermodynamic quantity of the targeted chemical species, it also frequently introduces new inconsistencies with previously established thermochemistry of other related species. Namely, their thermochemistry may have been obtained via sequential derivations that were pegged to the old value of the just revised species and should therefore be also revised: an essentially impossible task, since in tabulations obtained by sequential thermochemistry the intricate progenitorprogeny relationships are concealed. In addition, by virtue of pairing down competitive determinations by selecting what subjectively appears to be the "best" determination, traditional sequential thermochemistry chronically under-utilises the available thermochemically-relevant knowledge.

In fact, while in the case of CF and CF + the situation is relatively benign, there being available thermochemical values for CF that arguably appear reliable, things are veritably more complicated in the case of SiF and SiF + . Namely, the values for the enthalpy of formation of SiF available from the literature 24,25,29,[START_REF] Gurvich | Thermodynamic Properties of Individual Substances[END_REF][START_REF] Karton | [END_REF][77][78][79][80][81][82][83][84][85][86][87][88] encompass a spectacularly wide range, differing on the extremes by more than 16 kcal/mol, as demonstrated by Table 3. In principle, one might venture assuming that the values reported from the three most accurate electronic structure approaches [START_REF] Karton | [END_REF]81,82 are likely the most reliable. However, all three enthalpies of formation of SiF were derived from computations of the dissociation energy D 0 (SiF) and thus directly depend on the selected enthalpy of formation of Si atom. Notably, the recent introduction of key Si-containing chemical species in ATcT 39 has produced a significantly revised (and improved) value D f H 0 (Si) = 107.63 ± 0.14 kcal/mol, which can be compared with the generally accepted, but 1 kcal/mol lower (and substantially less accurate) value of 106.5 ± 1.9 kcal/mol derived by Gurvich et al., [START_REF] Gurvich | Thermodynamic Properties of Individual Substances[END_REF] recommended by CODATA, [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] and used in JANAF 88 and other tabulations. The older (and higher) value of 107.6 ± 0.1 kcal/mol found in the NBS Tables 86 is, in retrospect, in excellent agreement with the new ATcT value, as is the revised value of 107.2 ± 0.2 kcal/mol recently proposed by Karton and Martin. [START_REF] Karton | [END_REF] As opposed to the sequential thermochemistry approach, Active Thermochemical Tables rely on a different paradigm, rooted in constructing, statistically analysing, and solving a thermochemical network (TN) that contains all available determinations relevant to the thermochemistry of the included species, irrespective of whether they originate from experiment or high-level electronic structure theory. 37,38,89 The current public version of ATcT (ATcT TN ver. 1.124), [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] which contains nearly 2800 chemical species, has been developed within the context of several studies, such as the report on thermophysical and thermochemical properties of CH 2 and CH 3 using nonrigid rotor anharmonic oscillator (NRRAO) partition functions, 90 the development and benchmarking of a stateof-the-art computational approach that aims to reproduce total atomisation energies of small molecules within 10-15 cm 1 , 91 as well as the study of the reversible reaction 92 Since then, the underlying ATcT TN has been successively expanded to fulfil the needs of subsequent studies, such as those involving enthalpies of formation of key bromo-and iodomethanes, ethenes and ethynes, 93 the ring-opening dynamics of cyclopropyl and cyclopropylium (ATcT TN versions 1.128 and 1.130), 94 the bond dissociation energy and the adiabatic ionisation energy of CH (ATcT TN ver. 1.140), [START_REF] Thorpe | [END_REF] the role of methanediol in the atmosphere (ATcT ver. 1.148), [START_REF] Nguyen | Proc. Natl. Acad. Sci[END_REF] as well as a number of ongoing studies, eventually leading to the current developmental version ATcT TN 1.156. The latter contains more than 3150 species interconnected by over 30,000 thermochemically relevant determinations, but does not (yet) include the present experimental adiabatic ionisation energies.

C 2 H 3 + H 2 C 2 H 4 + H C 2 H 5 .
Although ATcT TN ver. 1.156 includes more than 350 new species and several thousand new determinations (a few of which do include CF or CF + as reactant or product), the thermochemistry of CF and CF + has remained nearly the same: D f H 0 (CF) = 58.124 ± 0.026 kcal/mol and D f H 0 (CF + ) = 268.41 ± 0.11 kcal/mol, the differences in comparison with the already discussed ATcT TN ver. 1.124 [START_REF] Ruscic | Active Thermochemical Tables (ATcT) values based on ver. 1.124 of the Thermochemical Network[END_REF] (less than 0.02 kcal/mol) comfortably contained within the associated (and slightly tighter) uncertainties. The resulting IE ad (CF) = 9.119 ± 0.005 eV is in agreement (within the combined uncertainties) with the current direct experimental value of IE ad (CF) = 9.128 ± 0.006 eV.

However, of particular relevance to the current study is that this version includes the SiF n , n = 1-4 group of species and their ions. Thus, ATcT TN ver. 1.156 produces D f H 0 (SiF) = 14.40 ± 0.15 kcal/mol and D f H 298 (SiF) = 13.97 ± 0.15 kcal/mol (where the 0 to 298.15 conversion exploits the 298.15 K enthalpy increments of SiF, 2.261 kcal/mol -slightly updated from Gurvich et al. [START_REF] Gurvich | Thermodynamic Properties of Individual Substances[END_REF] using the NASA PAC program [START_REF] Mcbride | Properties and Coefficients: Computer Program for Calculating and Fitting Thermodynamic Functions[END_REF] and spectroscopic constants from Huber and Herzberg, 57 crystal silicon, 0.769 kcal/mol, [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] and 1/2 of the already mentioned enthalpy increment for F 2 , 2.109 kcal/mol). [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] The matching 0 K dissociation energy of SiF is D 0 (SiF) = 6.093 ± 0.005 eV, and the corresponding BDE 298 (SiF) = 6.140 ± 0.005 eV. We note here that the ATcT value for D 0 (SiF) is significantly influenced by highly accurate state-ofthe-art W4 [START_REF] Karton | [END_REF] and FPD 81 calculations of the same quantity extant in the ATcT TN, and that the corresponding D f H 0 (SiF) makes use of the newly revised enthalpy of formation for gas-phase silicon atom, as already mentioned earlier, and which in this version of ATcT results amounts to D f H 0 (Si) = 107.63 ± 0.14 kcal/mol.

For the cation, ATcT TN ver. 1.156 produces D f H 0 (SiF + ) = 154.91 ± 0.39 kcal/mol and D f H 298 (SiF + ) = 155.18 ± 0.39 kcal/mol (where the conversion peruses the 298.15 K enthalpy increment of SiF + of 2.094 kcal/mol, as obtained from available spectroscopic constants 31,32,[START_REF] Huber | Molecular Spectra and Molecular Structure. IV. Constants of Diatomic Molecules[END_REF] by using the NASA PAC program [START_REF] Mcbride | Properties and Coefficients: Computer Program for Calculating and Fitting Thermodynamic Functions[END_REF] ). A variance decomposition analysis indicates that the primary con-

1-11 | 7
tributors to D f H (SiF + ) are the literature values for IE ad (SiF) included in the ATcT TN, combined with D f H (SiF), and only to a minor degree the theoretical D 0 (SiF + ), such as 159.58 (±1.5, estimated) kcal/mol. 77 Noting again that ATcT TN ver. 1.156 does not (yet) include the current experimental ionisation energies of CF and SiF, it is interesting to inspect the difference in ATcT 0 K enthalpies of formation of SiF + and SiF, which implies an adiabatic ionisation energy of SiF of 7.342 ± 0.016 eV. Curiously, while standard in-house midlevel composite methods extant in the TN suggest adiabatic ionisation energies ranging between 7.31 ± 0.10 eV (CBS-QB3) and 7.41 ± 0.08 eV (G4), with 7.36 ± 0.04 eV (W1) perhaps as a midpoint, the resulting ionisation energy is pushed toward the lower end of this range by the ostensibly accurate experimental value of 7.310 ± 0.011 eV 27,28 extracted from VUV absorption spectra, in spite of the fact that, based on a critical evaluation of those studies, the uncertainty initially assigned (a.k.a. 'prior') in the TN to this determination was double the uncertainty declared by the authors, and that the subsequent ATcT statistical analysis, which evaluates the internal consistency of the determinations in the TN, has further increased its uncertainty to ± 0.032 eV.

Clearly, the above IE ad of 7.342 ± 0.016 eV is appreciably less accurate than the current experimental IE ad (SiF) = 7.379 ± 0.009 eV, and it also appears inconsistent, given that the difference (0.037 eV) is significantly larger than the combined uncertainties. The normal course of action within the ATcT approach is to add the new results to the TN, and let the ATcT statistical analysis arbitrate between potentially inconsistent determinations.

The addition of the two experimental ionisation energies creates a new version, ATcT TN 1.158. The resulting thermochemical values of relevance to the present study are given in Table 4.

While the introduction of IE ad (CF) has not particularly affected the thermochemistry of neutral CF, with D f H (CF) and D 0 (CF) remaining essentially identical, it does affect and improve the thermochemistry of CF + , adjusting D f H 0 (CF + ) upward (by 0.113 kcal/mol) and becoming slightly more accurate (±0.089 kcal/mol, cf. to earlier ±0.11 kcal/mol). Importantly, the updated ATcT thermochemistry of the ion corresponds to D 0 (CF + ) = 7.790±0.004 eV and to IE ad (CF) = 9.124±0.004 eV, the latter being in excellent agreement with the very slightly higher experimental value of 9.128 ± 0.006 eV.

As one might have expected, the introduction of the experimental IE ad (SiF) into the ATcT TN has a more pronounced effect on the relevant species than the introduction of IE ad (CF). Also not surprisingly, the thermochemistry of neutral SiF is affected less than that of the ion, given that the former is constrained by D 0 (SiF) obtained from high-level electronic structure computations [START_REF] Karton | [END_REF]81 . Thus, D 0 (SiF) = 6.093 ± 0.005 eV, corresponding to 4 also includes the current ATcT values for the constituent atoms. Enthalpies of formation of atoms were considered as 'key' quantities already by CODATA, [START_REF] Cox | CODATA Key Values for Thermodynamics[END_REF] but since then they have gained additional importance, because they are needed to convert theoretically computed total atomisation energies to practical enthalpies of formation. While the genesis of the ATcT revision of the enthalpy of formation of C atom was discussed elsewhere, [START_REF] Changala | [END_REF] the new and improved ATcT enthalpy of formation of Si atom is formally given here for the first time.

Conclusion

In this study we presented photoelectron spectroscopic measurements of the first two group 14 monofluorides, CF and SiF, together with supporting quantum chemical calculations, further amplified by utilising the new experimental ionisation energies in conjunction with the Active Thermochemical Tables approach. The latter combination results in significant refinements of the related thermochemical properties, particularly those of SiF + , as well as those of CF + . The recommended new enthalpies of formation and dissociation energies of the neutral CF and SiF and their cationic counterparts, together with the resulting adiabatic ionisation energies, are summarised in Table 4.

Fig. 1

 1 Fig. 1 Mass-selected photoelectron signal of CF as a function of the photon energy (horizontal axis) and electron kinetic energy (vertical axis) for m/z 31. The corresponding total ion yield obtained by integrating over all electron energies is represented by the white curve.

  photon energy / eV

Fig. 2

 2 Fig.2Experimental threshold photoelectron spectrum of CF in the vicinity of the X + 1 S + X 2 P photoionising transition (in black) compared with our harmonic Franck-Condon calculation convolved with a Gaussian line shape (FWHM= 26 meV) at a vibrational temperature of 600K (in red). The red assignment corresponds to our harmonic calculation whereas the black comb follows the anharmonicity which allows an unambiguous attribution of the ionising transition towards v + = 11 (observed through autoionisation). See text for details.

Fig. 4

 4 Fig. 4 Mass-selected photoelectron signal of SiF as a function of the photon energy (horizontal axis) and electron kinetic energy (vertical axis) for m/z 47. The corresponding total ion yield obtained by integrating over all electron energies is represented by the white curve.

Fig. 5

 5 photon energy / eV 7.0 7.5 8.0 8.5 9.0 9.5 10.0 10.5 11.0

  D f H 0 (SiF) = 14.42 ± 0.15 kcal/mol, which is only marginally different than the value of 14.40 ± 0.15 kcal/mol from the preceding version of ATcT TN. However, the new and improved value for D f H 0 (SiF + ) is now 155.62 ± 0.24 kcal/mol, rather significantly different than the value of 154.91 ± 0.39 kcal/mol from the previous version. The new thermochemistry of SiF + corresponds to D 0 (SiF + ) = 6.872±0.009 eV and to IE ad (SiF) = 7.373±0.008 eV, in

b BDE 0

 0 (AB) is synonymous with D 0 (AB) c Recently revised value from ATcT, significantly improved over the CODATA 70 value of D f H 0 (Si) = 106.5 ± 1.9 kcal/mol and D f H 298 (Si) = 107.6 ± 1.9 kcal/mol; see text superb agreement with the experimental value of 7.379±0.009 eV. For reference purposes, Table

Table 1

 1 Calculated and experimental equilibrium spectroscopic properties of the ground electronic states of CF, CF + , SiF, and SiF + . See text for details.

		r e / Å	w e /cm 1	w e x e /cm 1	w e y e /cm 1	Ref.
	CF	1.2731	1303.06	10.76	0.08	calc.
	CF +	1.1558	1773.21	13.16	0.05	calc.
			1786.5	11.89		exp.
		1.154	1810			16
		1.1542551 1792.6654 13.229668		18
	SiF	1.6143	833.16	4.45	0.02	calc.
	SiF + 1.5394	1024.44	4.69	0.01	calc.
			1056.8	5.17		exp.
		1.5264950 1050.7			31
		1.52652	1050.3757 4.9462		32

Table 2

 2 Calculated and experimental adiabatic ionisation energies of the X + 1 S + X 2 P photoionising transition of CF and SiF. See text for details.IE ad IE ad,corrZPE IE ad,exp.

		/eV	/eV	/eV	Ref.
	CF	9.029	9.059	9.128	this work
				9.11	15,16
	SiF 7.325	7.337	7.379	this work
				7.54	24
				7.08	25
				7.31	26
				7.31	28

Table 3

 3 Compilation of prior literature values for the SiF enthalpies of formation at 0 K and 298 K, D f H 0 (SiF) and D f H 298 (SiF), in kcal/mol.

	D f H 0 (SiF)	D f H 298 (SiF)	Refs.
	12.70 ± 3.0 11.7 ± 2.1	14.2 ± 2.0 12.42 ± 3.0 5 ± 3 11.2 ± 2.1 13.4	78 (theory) 79 (theory) 24 (exp) 25 (exp) 80 (theory)
	14.8 ± 0.4 14.9 ± 0.3 14.79	14.0 ± 2.0 13.90 ± 0.35 14.36	29,77 (theory) 81 (theory) 71 (theory) 82 (theory) 83 (theory)
	15.25 ± 2.00 14.4	14.95 ± 2.00	84 (theory) 85 (theory)
	1.0 ± 1.0 5.2 ± 3.0 6.5 ± 2.6	1 .7 ± 1.0 5 ± 6 4.8 ± 3.0 6.0 ± 2.6	86 (eval) 87 (eval) 88 (eval) 69 (eval)

Table 4

 4 Recommended thermochemical values for CF, SiF, and their cations from ATcT TN ver.1.158

	Quantity	0 K	298.15 K	Uncert.	Units
	D f H T (CF) D f H T (CF + ) IE ad (CF)	58.123 268.522 9.124 (9.128) a	58.984 269.290	±0.026 ±0.089 ±0.004 (±0.006) a	kcal/mol kcal/mol eV eV
	BDE T (CF) b BDE T (CF + ) b	5.653 7.790	5.695 7.836	±0.001 ±0.004	eV eV
	D f H T (SiF) D f H T (SiF + ) IE ad (SiF)	-14.42 155.62 7.373 (7.379) a	-13.98 155.89	±0.15 ±0.24 ±0.008 (±0.009) a	kcal/mol kcal/mol eV eV
	BDE T (SiF) b BDE T (SiF + ) b	6.093 6.872	6.141 6.924	±0.005 ±0.009	eV eV
	D f H 0 (C) D f H 0 (C + ) D f H 0 (F) D f H 0 (Si) c D f H 0 (Si + )	170.029 429.697 18.464 107.63 295.62	171.340 431.035 18.967 108.67 296.60	±0.010 ±0.010 ±0.004 ±0.14 ±0.14	kcal/mol kcal/mol kcal/mol kcal/mol kcal/mol

a Current experimental adiabatic ionisation energy

[1][2][3][4][5][6][7][8][9][10][11]

Acknowledgments

This work was performed on the DESIRS Beamline at SOLEIL synchrotron under project numbers 20200996 and 20140832. The work at Argonne National Laboratory (B.R.) was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division, under Contract No. DE-AC02-06CH11357, through the Gas-Phase Chemical Physics Program. The authors are grateful to the whole staff of SOLEIL for running the facility. Ning L. Chen acknowledges the support from the Paris Ile-de-France Region (DIM ACAV+) for her Ph.D. grant. This work has also received financial support from the French "Agence Nationale de la Recherche" (ANR) under Grant No. ANR-12-BS08-0020-02 (Project SYNCHROKIN). This work was supported by the Programme National "Physique et Chimie du Milieu Interstellaire" (PCMI) of CNRS/INSU with INC/INP cofunded by CEA and CNES. The Active Thermochemical Tables are a U.S. Department of Energy Office of Science Public Reusable Research (DOE SC PuRe) Data Resource. 98 Notes and references

Conflicts of interest

There are no conflicts to declare.


Sophie Mieszkin
email: sophie.mieszkin@univ-brest.fr

Blandine Trouche

Julien Ancousture

Youssef Raouf

Stéphane Uroz

Karine Alain

Scleromatobacter humisilvae gen. nov., sp. nov., a novel bacterium isolated from an oak forest soil

Keywords: Scleromatobacter humisilvae, Betaproteobacteria, Burkholderiales, Comamonadaceae, oak forest soil AAI, Average Amino acids Identity, AF, Alignment Fraction, ANI, Average Nucleotide Identity, CAPSO, N-cyclohexyl-3-aminopropanesulfonic acid, COGs, cluster of orthologous groups, dDDH, Digital DNA-DNA hybridization, DMSO, dimethyl sulfoxide, DPG, diphosphatidylglycerol, DSMZ, Deutsche Sammlung TEM, Transmission Electron Microscopy, TSA, Tryptic

A novel bacterial strain, designated BS-T2-15 T , isolated from forest soil in close proximity to decaying oak wood, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences as well as phylogenomic analyses based on coding sequences of 340 concatenated core proteins indicated that strain BS-T2-15 T forms a distinct and robust lineage in the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch of the order Burkholderiales. The amino acid identity (AAI) and the percentage of conserved proteins (POCP) between genome of strain BS-T2-15 T and genomes of closely related type strains ranged from 54.27 to 66.57% and from 43.17 to 49.27%, respectively, providing genomic evidence that strain BS-T2-15 T represents a new genus. Its cells stain Gram-negative, are aerobic, motile by a polar flagellum, rodshaped and form incrusted white to ivory colonies. Optimal growth is observed at 20-22°C, pH 6 and 0% NaCl. The predominant fatty acids of strain BS-T2-15 T are C 16: 1 ω7c, C 16:0 and C 14:0 2-OH. Its polar lipid profile consists of a mixture of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol and its main respiratory quinone is ubiquinone 8. The estimated size of its genome is 6.28 Mb with a DNA G+C content of 69.56 mol%. Therefore, on the basis of phenotypic and genotypic properties, the new strain BS-T2-15 T represents a new genus and a novel species for which the name Scleromatobacter humisilvae gen. nov., sp. nov., is proposed. The type strain is BS-T2-15 T (DSM 113115 T =UBOCC-M-3373 T ).

In forest ecosystems, wood decay is an important process that participates to the soil fertility through the action of a complex guild of decomposers [START_REF] Ulyshen | Wood decomposition as influenced by invertebrates[END_REF][START_REF] Tláskal | Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition[END_REF]. Among them, fungi are considered as the main actors, while the role of bacteria is much less documented [START_REF] Johnston | Bacteria in decomposing wood and their interactions with wood-decay fungi[END_REF]. To fill this gap, the taxonomic diversity and the metabolic and functional potential of bacterial strains isolated from a soil-decaying-wood continuum have been investigated [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF]. Overall, this study demonstrated a community dominated by representatives of the genera Paraburkholderia (Betaproteobacteria), Streptomyces, Kitasatospora, Arthrobacter and Streptacidiphilus (Actinobacteria), Dyella (Gammaproteobacteria) and by uncharacterized bacterial strains [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF]. At the functional level, this study also revealed that soil bacterial communities have the potential to decompose organic matter and a stronger effectiveness than those isolated from decaying oak wood. The taxonomic assignation and functional screening allowed the identification of various strains of interest, among which strain BS-T2-15 T , one of the uncharacterized strains, was selected to be further characterized in the present study to clarify its taxonomic position within the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch of the order Burkholderiales, in the class Betaproteobacteria. To date, there is a taxonomic uncertainty regarding the classification of these genera at the family rank level.

Recently, Liu et al. [START_REF] Liu | Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions[END_REF] proposed to refer to this branch as the closest-to-Comamonadaceae (CTC) group, as it forms a phylogenetically coherent group close to genera belonging to the Comamonadaceae family. They proposed to classify the CTC group as a new family, 'Sphaerotilaceae' fam. nov., based on phylogenomic analyses, genome relatedness indices and phenotypic data. However, this new delineation is not yet recognized by the International Committee on Systematics of Prokaryotes (ICSP). In addition, they also proposed several taxonomic revisions at the genera and species levels. Among remarkable physiological features of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch, some species are known to be involved in the biodegradation of petroleum compounds or in the reduction of chlorate to chloride under anaerobic conditions [START_REF] Bedics | Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions[END_REF][START_REF] Lechner | Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium[END_REF][START_REF] Malmqvist | Ideonella dechloratans gen. nov., sp. nov., a new bacterium capable of growing anaerobically with chlorate as an electron acceptor[END_REF].

In the present study, we performed a polyphasic taxonomic characterization of strain BS-T2-15 T and provided phenotypic, phylogenomic, and genomic evidences that it meets the criteria for delineating a new species of a new genus within the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch. We propose to name this new species Scleromatobacter humisilvae gen. nov., sp. nov.

ISOLATION AND ECOLOGY

Strain BS-T2-15 T is from a collection of 308 bacterial strains established as part of a study on the functional abilities of bacterial isolates from decaying wood and their comparison with the properties of bacteria from underlying soil [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF]. The experimental set up consisted in oak discs that have been placed during 9 months on the soil surface of the forest experimental site of Champenoux (north-eastern France; Lat: 48.718420° N; Long: 6.346580° E; Alt: 248 m; 0.5 ha of surface). Strain BS-T2-15 T was isolated from the bulk soil in direct contact with decaying oak disc by serial dilutions on 1/10 diluted Tryptic Soy Agar (TSA) medium (Difco's Tryptic Soy Broth (TSB) 3 g.L -1 and agar 15 g.L -1 ) containing cycloheximide (100 g.L -1 , final concentration), with a pH adjusted to 5. The strain was then purified by 3 successive spreads on 1/10 diluted TSA plates at pH 5 to obtain a pure culture. The strain BS-T2-15 T was then grown routinely on 1/10 TSA or 1/10 TSB media adjusted to pH 5 during 3 days at 20°C, under agitation (250 rpm). Its purity was routinely confirmed by microscopic observations, and by sequencing of its 16S rRNA gene and genome.

Stock cultures were stored at -80°C in 1/10 TSB medium supplemented with 5% (v/v) dimethylsulfoxide (DMSO). Main chemical characteristics of the bulk soil samples were pH 4.65 ± 0.10, 48.38 ± 7.93 g.kg -1 total carbon, 3.26 ± 0.49 g.kg -1 total nitrogen, 0.17 ± 0.01 g.kg -1 phosphorus extracted according to the Duchaufour method and 83.80 ± 13.92 g.kg -1 organic matter [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF].

Strain BS-T2-15 T (DSM 113115

MORPHOLOGY AND PHYSIOLOGY

Colony morphology of the isolate BS-T2-15 T was observed on 1/10 TSA adjusted to pH 6. Cell morphology and motility were determined by light microscopy (Olympus BX60 and CX40) and transmission electron microscopy (TEM; JEOL JEM 1400).

Motility was also observed by using the Mannitol-Motility-Nitrate agar medium (MMN, composed (per liter) of 10 g tryptic hydrolysate of casein, 1 g potassium nitrate, 7.5 g mannitol, 40 mg phenol red and 3.5 g agar), which was also used to evidence mannitol fermentation and nitrate reductase activity. Gram-staining was determined using standard procedures and confirmed with a KOH (3%) test. Catalase and cytochrome oxidase activities were respectively evaluated using H 2 O 2 and strips of N, N, N',N'-tetramethyl-p-phenylenediamine dihydrochloride (Bio-Rad). The oxidase test was repeated several times using independent cultures to confirm the result.

Colonies of BS-T2-15 T are circular and rough with a color between white and ivory. A major phenotypic feature is that its colonies are incrusted in the agar medium. the observation of a single polar flagellum per cell by TEM (Fig. 1C,D). Refringent intracellular granules, which could be polyhydroxyalkanoates (PHA) storage granules, were also observed (Fig. 1A). The strain is catalase positive and oxidase negative. The latter phenotypic feature clearly distinguishes strain BS-T2-15 T from other genera of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch which are all oxidase positive. However, it is important to note that, cytochrome C oxidase complex was identified in its genome. This point is discussed latter in the study.

Physiological characterization of the novel strain BS-T2-15 T was carried out aerobically, in triplicate, on 1/10 TSA or TSB adjusted to pH 6 at 20°C and under agitation (250 rpm). Determination of the temperature range for growth and salt tolerance were respectively tested over the range 0-45°C, at 5°C intervals and 0-10% NaCl (w/v), at 0.5% intervals, both for 10 days on 1/10 TSA at pH 6. Growth was observed from 4 to 30°C with optimal growth between 20-22°C. Concerning salt tolerance, the strain grew only at 0.5% NaCl and exhibited an optimal growth without sodium chloride. The pH range for growth was tested from pH 2.0 to pH 12 (at 20°C), with increments of 1 unit on 1/10 TSB medium for 8 days. Cells were routinely enumerated by direct cell counting using a modified Thoma chamber (Preciss, France; surface: 0.0025 mm 2 , depth: 10 µm). The following buffers (each at 20 mM, Sigma-Aldrich, Darmstadt, Germany) were used to adjust the required pH: pH 4.0 and 5.0 with HOMOPIPES buffer, pH 6.0 with MES buffer, pH 7.0 with PIPES buffer, pH 8.0 with HEPES buffer, and pH 9.0 and 10.0 with CAPSO buffer. For pH 2.0, 3.0, 11.0 and 12.0, no buffer was used. Growth of strain BS-T2-15 T was observed from pH 2.0 to 12 with optimal growth at pH 6. The growth kinetics of BS-T2-15 T under optimal conditions was then studied in triplicates, on 1/10 TSB adjusted to pH 6 at 22°C with no NaCl salt, under agitation (250 rpm) for 4 days. Cell growth was monitored by direct cell counting, every 3 h using a modified Thoma chamber, in order to determine the growth rate and doubling time of the strain under optimal culture conditions. The growth rate and the generation time of strain BS-T2-15 T are respectively, 0.17 h -1 and 3 h 58 min.

Utilization of carbon sources was investigated using the mineral basis of the 1/10 TSB medium containing (L -1 ): 0.25 g KH 2 PO 4 and adjusted at pH 6. Each substrate (lactose, D-mannose, D-ribose, D-maltose, D-glucose, N-acetylglucosamine, butyric acid, gluconate, citrate, benzoate, acetate, pyruvate and urea) was supplied at a final concentration of 20 mM. Utilization of nitrogen sources was investigated using 1/10

TSB medium adjusted at pH 6 with nitrate and ammonium supplied at a final concentration of 20 mM, while nitrite was supplied at a final concentration of 5 mM.

Before inoculation, cells at the end of their exponential growth phase were harvested and washed three times with distilled water and then the bacterial suspension was adjusted to obtain a Mac Farland index value of 1. A medium composed of mineral basis of the 1/10 TSB without carbon source was used as negative control for each carbon utilization bioassay and a positive control was performed using 1/10 TSB medium adjusted at pH 6. The hydrolysis of cellulose was determined using

Carboxymethyl Cellulose (CM Cellulose) as described by Mieszkin et al. [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF]. These tests were completed with liquid or solid cultures allowing to determine: (i) mannitol fermentation and presence of nitrate reductase (MMN agar medium), (ii) fermentative pathways (mixed acids or butane-2,3-diol pathways; Clark and Lubs liquid medium), (iii) glucose and lactose fermentation, gas and H 2 S production (Kligler-Hajna agar medium), and, (iv) citrate utilization (Simmons citrate agar medium). For these assays, culture media, cell cultures and washes and preparation of bacterial suspensions were performed as described above and by Mieszkin et al. [START_REF] Mieszkin | Acidisoma silvae sp. nov. and Acidisoma cellulosilytica sp. nov., two acidophilic bacteria isolated from decaying wood, hydrolyzing cellulose and producing poly-3-hydroxybutyrate[END_REF]. Strain BS-T2-15 T is chemoorganoheterotrophic and grows by aerobic respiration. It catabolizes D-glucose, lactose and pyruvate while a moderate growth was obtained with D-ribose, N-acetylglucosamine, urea and gluconate. A weak growth was also observed with all the nitrogen substrates tested (nitrate, nitrite and ammonium). In addition, BS-T2-15 T is capable of using nitrate or nitrite as terminal electron acceptors showing that the nitrate reductase is functional (Table 1).

Volatile fatty acid production of strain BS-T2-15 T after growth in duplicate in 1/10 TSB was assessed by high-pressure ion chromatography (Dionex ICS-6000 HPIC) (Growth conditions: pH 6, 20°C, under agitation (250 rpm), for 3 days). HPIC analyses showed that the strain consumed all the pyruvate present in the medium during its growth (approximately 930 µM), but did not produce acetate, lactate, pyruvate or oxalate under these culture conditions. This is consistent with previous results showing that it is capable to grow with pyruvate as sole carbon source.

Strain BS-T2-15 T was not capable to use chlorate as sole terminal electron acceptor (at 20 mM), when grown anaerobically on 5 g.L -1 NaCl, with 1 g.L -1 tryptone as carbon and energy source (with respect to negative and positive controls).

Sensitivity to antibiotics of strain BS-T2-15 T was tested by the disc diffusion method days of incubation at 20°C. Among the antibiotics tested, strain BS-T2-15 T was sensitive to kanamycin, novobiocin, gentamicin and streptomycin.

CHEMOTAXONOMY

In order to analyze respiratory quinones, polar lipids, and fatty acids, cells of strain BS-T2-15 T were cultured in 1/10 TSB pH 6 at 20°C under agitation (250 rpm) and then harvested by centrifugation (800 g; 10 min) at the end of their exponential phase of growth. These analyses were carried out by the Identification Service of the DSMZ (Braunschweig, Germany) as described by Tindall [START_REF] Tindall | A comparative study of the lipid composition of Halobacterium saccharovorum from various sources[END_REF][START_REF] Tindall | Lipid composition of Halobacterium lacus profundi[END_REF] and Kuykendall et al. [START_REF] Kuykendall | Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum[END_REF].

The major respiratory quinone identified for strain BS-T2-15 T is ubiquinone 8 (Q-8).

The polar lipid profile of the novel isolate consisted in phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). A common feature of the new strain and species belonging to the related genera Leptothrix, Rubrivivax, Ideonella and Aquincola is the high proportion of PE and PG, which is consistent with the Comamonadaceae family [START_REF] Jeon | Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment[END_REF][START_REF] Blümel | Xenophilus azovorans gen. nov., sp. nov., a soil bacterium that is able to degrade azo dyes of the Orange II type[END_REF]. However, a major characteristic of strain BS-T2-15 T is its high content of DPG, a polar lipid that is absent or only present in low proportions in the type strains of the closest genera (Table S1 et Fig. S1).

The predominant cellular fatty acids (>10% of the total fatty acids) of strain BS-T2-15 T are C 16:1 ω7c (40.45%), C 16:0 (25.18%) and C 14:0 2-OH (10.49%) (Table 2).

Noticeably, the main saturated fatty acid detected (i.e., C 16:0 ) appeared dominant and common among BS-T2-15 T and the four closely related genera (Leptothrix, Rubrivivax, Ideonella and Aquincola), while the hydroxyl fatty acid (i.e. C 14:0 2-OH) was only detected in strain BS-T2-15 T (Table 1). In addition, the presence of the unsaturated fatty acid C 16:1 ω7c is another major feature of the new strain but could also be represented by summed feature 3 (C16: 1 ω7c o and/or C16: 1 ω6c) in Rubrivivax gelatinosus DSM 1709 T and Ideonella dechloratans CGUG 30977 T .

16S rRNA GENE PHYLOGENY

A full 16S rRNA gene sequence (1512 nt) of strain BS-T2-15 T was extracted from the genome using the bacterial ribosomal predictor tseemann/barrnap on Galaxy v1.2.1 [START_REF] Seemann | BARNAP: BAsic Rapid Ribosomal RNA Predictor[END_REF]. Pairwise 16S rRNA gene sequence similarity was calculated using the global alignment algorithm implemented at the EzTaxon-e server (http://eztaxone.ezbiocloud.net/; [START_REF] Yoon | Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies[END_REF]). Phylogenetic analyses were performed using the software Seaview version 4.7 for trees reconstruction by the neighbor-joining (NJ) and maximum parsimony (MP) methods [START_REF] Gouy | SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building[END_REF][START_REF] Saitou | The neighbor-joining method: A new method for reconstructing phylogenetic trees[END_REF][START_REF] Kimura | The Neutral Theory of Molecular Evolution[END_REF]. The evolutionary distances were respectively calculated using the Kimura two-parameters and the Dnapars modes.

The robustness of the inferred topology was assessed by bootstrap analyses based on 1,000 replications. A third tree was build using the maximum likelihood (PhyML) method with the subtree-pruning-regrafting algorithm (http://phylogeny.lirmm.fr/phylo_cgi/simple_phylogeny.cgi) [START_REF] Dereeper | Phylogeny. fr: robust phylogenetic analysis for the non-specialist[END_REF][START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[END_REF]. The 16S rRNA gene sequence analysis of strain BS-T2-15 T showed that it belongs to the class Betaproteobacteria, the order Burkholderiales and the family Comamonadaceae. The NJ and MP phylogenetic trees based on 16S rRNA gene sequences revealed that strain BS-T2-15 T does not form a monophyletic clade with any representatives of related taxa (Fig. S2 andS3). However, most of the bootstrap percentages of the trees had a very low value (<70%). Concerning the PhyML tree, a clade was obtained with strain BS-T2-15 T and Leptothrix mobilis (Feox-1; X97071) but it was distantly related to most of the genera of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch (Fig. S4).

Comparative analysis of the 16S rRNA gene sequence of the novel strain with relatives having validly published names showed that BS-T2-15 Overall, these results demonstrate that the 16S rRNA gene-based phylogeny lacks of resolution to evaluate the taxonomic position of strain BS-T2-15 T among the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch, as previously underlined by Liu et al. [START_REF] Guindon | New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0[END_REF]. Genome based phylogeny is therefore mandatory to gain a better resolution to assign with certainty the taxonomic position of the new strain BS-T2-15 T .

GENOME FEATURES

Genomic DNA of strain BS-T2-15 T was extracted with a standard PCI (Phenol:

Chloroform: Isoamyl Alcohol (25:24:1)) protocol [START_REF] Charbonnier | Purification of plasmids from thermophilic and hyperthermophilic archaebacteria[END_REF] 5.38%). Then, 24.56% of CDSs were allocated to the COGs category related to cellular process and signaling and the following processes were dominant: signal transduction mechanisms (T; 7.64%) and cell wall, membrane and envelope biogenesis (M; 5.26%). Finally, 14.91% of the CDSs were predicted to be involved in the processes dedicated to the information storage and processing (Table S2).

In addition to phylogenetic trees based on the 16S rRNA sequences that do not provide robust phylogenetic reconstructions with this dataset, a phylogenomic tree for was constructed based on 340 core gene clusters (gene clusters appearing once in each genome).

This tree encompassed 21 reference genomes representative of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch and phylogenetically related to strain BS-T2-15 sulfidivorans D-507 T ), the target genome BS-T2-15 T and two closely related Metagenome Assembled Genomes (MAGs; from the Genome Taxonomy Database (GTDB, https://gtdb.ecogenomic.org/); accession numbers GB_GCA_013289985.1 and GB_GCA_903845345.1) artificially classified as genus CAIMXF01. These closely related MAGs were respectively recovered from a forest soil [START_REF] Alteio | Complementary metagenomic approaches improve reconstruction of microbial diversity in a forest soil[END_REF] and from stratified freshwater lakes and ponds [START_REF] Martin | Candidatus Methylumidiphilus drives peaks in methanotrophic relative abundance in stratified lakes and ponds across Northern landscapes[END_REF][START_REF] Garcia | Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations[END_REF][START_REF] Rissanen | Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes[END_REF]. The phylogenomic tree was built as follows: (i) amino acid sequences were extracted, aligned and concatenated using command line anvi-get-sequences-for-gene-clusters on Anvi'o v. 7.1 [START_REF] Eren | Community-led, integrated, reproducible multi-omics with anvi'o[END_REF], then (ii) positions with over 0.5 gap frequency were masked, and finally (iii) a maximum likelihood tree was computed using IQTREE (v2.0.3, [START_REF] Hoang | UFBoot2: improving the ultrafast bootstrap approximation[END_REF][START_REF] Minh | IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era[END_REF]) under the model WAG with 1,000 ultrafast bootstrap replicates (See SI for more details). The tree was rooted using the genome of Alcaligenes faecalis ZD02 (GCA_000967305.2) as an outgroup. A second phylogenomic tree was built by placing BS-T2-15 T in the GTDB tree using GTDB-tk (v2.1, [START_REF] Chaumeil | GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database[END_REF]), then subsetting the tree to family Burkholderiaceae and genus Escherichia, extracting the amino acid alignment, masking positions with over 0.5 gap and computing a maximum likelihood (ML) tree with IQTREE under the model WAG as described above. This second tree was built with 229 MAGs and 60 cultivated bacterial strains from the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch.

The phylogenomic tree built with the 21 reference genomes and the two MAGs closely related to strain BS-T2-15 T , was very robust with high ultrafast bootstrap values, and showed a distinctly deeper branching of strain BS-T2-15 T with its two closely related MAGs and a close proximity to the Ideonella clade (Fig. 2). A similar result was also obtained with the phylogenomic tree built with the 229 MAGs (Fig. S6). Therefore, these two phylogenomic trees indicate that strain BS-T2-15 T indeed represents a new genus of the Comamonadaceae family within the order Burkholderiales, and belongs to the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch.

In addition to the phylogenomic trees, Overall Genome Related Indices (OGRI) were obtained by pairwise calculations between genome of strain BS-T2-15 T , the two closely related MAGs of strain BS-T2-15 T and the 21 reference genomes. The average nucleotide identity scores (ANI) were obtained using the FastANI calculator tool from the GTDB web server (https://gtdb.ecogenomic.org/tools/fastani) [START_REF] Jain | High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries[END_REF]. In addition, FastANI calculator provided also the alignment fraction (AF) values between genomes. Digital DNA-DNA hybridization (dDDH) scores were determined by the genome-to-genome distance calculator (GGDC 2.1), using formula 2 [START_REF] Meier-Kolthoff | Genome sequence-based species delimitation with confidence intervals nd improved distance functions[END_REF]. The average amino acid identity (AAI) calculations between genomes were determined as described by Kim et al. [START_REF] Kim | Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity[END_REF] using the EzAAI pipeline (http://leb.snu.ac.kr/ezaai). The percentage of conserved proteins (POCP) was estimated as described by Qin et al. [START_REF] Qin | A proposed genus boundary for the prokaryotes based on genomic insights[END_REF].

Digital DNA-DNA hybridization and ANI values between the strain BS-T2-15 T genome and the genomes of type strains of the closest genera ranged from 20.00 to 20.50% and from 78.50 to 79.70%, respectively (Table 3). These values are both far below the dDDH threshold level of 70% and the ANI value of 95-96% that are generally accepted for species delineation [START_REF] Richter | Shifting the genomic gold standard for the prokaryotic species definition[END_REF][START_REF] Wayne | Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics[END_REF]. Concerning the AAI and POCP values between genome of strain BS-T2-15 T and genomes of the type strains of the closest genera, they ranged, respectively, from 64.27 to 66.57% and from 43.17 to 49.27% (Table 3). AAI values are close to the 65% cutoff value generally accepted for delineating a new genus, while POCP values are below the 50% threshold recognized for demarcating a new genus [START_REF] Qin | A proposed genus boundary for the prokaryotes based on genomic insights[END_REF][START_REF] Konstantinidis | Uncultivated microbes in need of their own taxonomy[END_REF]. Finally, the AF values ranged between 0.40 and 0.48 between genomes of strain BS-T2-15 T and type strains of the closest genera (Table 3), and were observed in conjunction with low ANI values [START_REF] Barco | A genus definition for bacteria and archaea based on a standard genome relatedness index[END_REF], the new strain BS-T2-15 T is the only one with the genetic potential to achieve the biosynthesis of betaxanthin (a secondary metabolite) and to degrade alanine and anthranilate (Table S9).

which
In conclusion, from the clear genotypic distance with the closest genera, the physiological similarities and some phenotypical and chemotaxonomic differences, we comply with the phylo-phenetic concept that currently prevails for the description of a new genus. Thus, we assigned strain BS-T2-15 List of tables: Table 1. Differential characteristics of strain BS-T2-15 T and type strains of closely related genera.

Taxa : 1. BS-T2-15 T , 2. Leptothrix mobilis DSM 10617 T , 3. Rubrivivax gelatinosus DSM 1709 T , 4. Ideonella dechloratans CGUG 30977 T , 5. Aquincola tertiaricarbonis DSM 18512 T . Data are from Mieszkin et al. [START_REF] Mieszkin | Oak decaying wood harbors taxonomically and functionally different bacterial communities in sapwood and heartwood[END_REF], Lechner et al. [START_REF] Lechner | Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium[END_REF], Malmqvist et al. [START_REF] Malmqvist | Ideonella dechloratans gen. nov., sp. nov., a new bacterium capable of growing anaerobically with chlorate as an electron acceptor[END_REF], Chen et al. [START_REF] Chen | Ideonella livida sp. nov., isolated from a freshwater lake[END_REF], Sheu et al. [START_REF] Sheu | Aquincola rivuli sp. nov., isolated from a freshwater stream[END_REF], Spring et al. [START_REF] Spring | Polyphasic characterization of the genus Leptothrix: new descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend[END_REF] and Willems et al. [START_REF] Willems | Transfer of Rhodocyclus gelatinosus to Rubrivivax gelatinosus gen. nov., comb. nov., and phylogenetic relationships with Leptothrix, Sphaerotilus natans, Pseudomonas saccharophila, and Alcaligenes latus[END_REF]. +, Positive; -, negative; NA, not available; w, weak growth; a Summed feature 3 comprises C16: 1 ω7c and/or C16: 1 ω6c. All strains are motile, positive for tween 40 hydrolysis, and negative for urease activity and citrate utilization. § As all strains have not been grown under exactly the same conditions nor in the same media, percentages of fatty acids cannot be compared from one strain to another.

  after spreading cell suspensions (1 McFarland) on 1/10 TSA adjusted to pH 6 at 20°C for 7 days. Discs were impregnated with antibiotic solutions to obtain a final quantity of antibiotic per disc of: kanamycin (40μg), rifampicin (30 μg), novobiocin (30 μg), gentamicin (15 μg), ampicillin (10 μg), penicillin (10 U), oxacillin (5 μg), oxytetracycline (30 μg), chloramphenicol (30 μg), and streptomycin (10 μg). The discs were then placed on the agar surface. The inhibition zones were read after 3

  is not incompatible with the description of a new genus. In this case, POCP and, to a lesser extent, ANI, are the most relevant indices to demonstrate that strain BS-T2-15T represents a new genus. Similar results were obtained when considering the 21 reference genomes (Fig.S7and Tab. S3). In addition, all OGRI values obtained between the BS-T2-15 T strain genome and the genomes of its two closely related MAGs were higher compared to the values obtained against genomes of cultured type strains. These OGRI values relative to the closest MAGs were respectively in the range of 30.10-40.40% and 87.40-88.90% for dDDH and ANI, and in the range of 84.14-86.43%, 70.[START_REF] Richter | Shifting the genomic gold standard for the prokaryotic species definition[END_REF]-74.76% and 0.70-0.80 for AAI, POCP and AF indices (Tab S4-S8). These dDDH and ANI values are below the threshold accepted for species delineation while the AAI, POCP and AF values are above the threshold for a new genus delineation. Overall, these OGRI analyses clearly show that strain BS-T2-15 T and its two closely related MAGs (i) belong to the same genus, (ii) represent a new genus of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch and, (iii) belong to three distinct genomic species. Furthermore, values of the different OGRI indices calculated between the species of the genus Ideonella and strain BS-T2-15 T and its two closely related MAGs are much lower than those obtained between strain BS-T2-15 T and its two closely related MAGs (Tab S4-S8). Thus, OGRI indices, as well as phylogenomic analyses, lead all to the conclusion that strain BS-T2-15 T represents a new species of a new genus of the Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch. For gene function prediction, genome annotations were performed with the MaGe platform using KEGG and BioCyc databases. The genome of the new strain BS-T2-15 T encodes metabolic pathways for organoheterotrophic growth. Notably, the genome encodes a complete pentose phosphate pathway, and a complete Entner-Doudoroff pathway. The tricarboxylic acid cycle (TCA) pathway for aerobic respiration is almost complete (one enzyme missing

Figure 1 .

 1 Figure 1. Transmission electron micrographs of cells of strain BS-T2-15 T showing (A) intracellular granules (indicated by black arrows), (B) a dividing cell (by binary fission), (C) a cell with its polar flagellum, and (D) the insertion point of the flagellum.

Fig. 2 .

 2 Fig. 2. Phylogenomic tree (concatenated alignment of 340 shared gene clusters) showing the phylogenomic position of strain BS-T2-15 T , its two closely related MAGs and representatives of other related taxa. The tree was built using IQ-Tree and the maximum likelihood method with 1,000 replicates for the calculation of the ultrafast bootstrap. Bootstrap values >95% are indicated at branching point by a dot. The tree was rooted using Alcaligenes faecalis ZD02 (GCA_000967305.2) as the outgroup. Bar, 0.04 substitutions per position.

  T = UBOCC-M-3373 T ) is available in the public culture collections Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ;

	https://www.dsmz.de/collection)	and	UBO	Culture	Collection	(UBOCC;

https://www.univ-brest.fr/ubocc).

  To our knowledge, this was not yet reported in the literature for genera belonging to the

	Rubrivivax-Roseateles-Leptothrix-Azohydromonas-Aquincola-Ideonella branch. Cells
	are Gram-negative coccobacilli that divide by binary fission and occur mainly singly,
	but can also form aggregates (Fig. 1A, B). Cell size range from 0.59 to 0.93 µm wide
	(mean 0.78 µm; n=45) and from 1.71 to 2.73 µm long (mean 2.15 µm; n=45). Strain
	BS-T2-15 T is motile, as confirmed by growth observations on MMN agar medium and

  ). The genome of the novel isolate encodes also the nitrate VIII reduction pathway (dissimilatory) for anaerobic nitrate respiration, which has been shown to be functional experimentally.

	Degradation pathways for organic compounds such as amino acids (alanine,
	arginine, asparagine, serine, glutamine, glycine, histidine, cysteine, lysine, ornithine,
	taurine, threonine and tryptophan), carbohydrates (acetoin, chitin, glucose, glucose-
	1-phosphate, lactose, ribose and xylose), aromatic compounds (anthranilate,
	gentisate, phenylacetate and protocatechuate), alcohols (ethanol and glycerol),
	aldehyde (L-lactaldehyde), amines and polyamines (choline, 4-aminobutyrate,
	ethanolamine and urea), and carboxylates (D-gluconate, glutaryl CoA, glycolate and
	glyoxylate) are evidenced. The cytochrome C oxidase complex (EC number: 7.1.1.9;
	locus tags: COMBST215_v1_20371; 20374; 20375; 20376; 80152; 80156; 80157)
	was also identified despite that the oxidase activity not being demonstrated
	experimentally. The cyclopropane fatty acid (CFA) biosynthesis via the cyclopropane-
	fatty-acyl-phospholipid	synthase	(EC	number:	2.1.1.79;	locus	tag:
	COMBST215_v1_10589; 50189) and the arginine dependent acid resistance
	(arginine decarboxylase; EC number: 4.1.1.19; locus tag: COMBST215_v1_10270)
	pathways are present and may give the strain a competitive advantage in acidic
	environments such as the forest soil ecosystem. The new strain BS-T2-15 T has also
	the genetic potential to detoxify arsenate using glutaredoxin (gene: arsC; EC number:
	1.20.4.1; locus tag: COMBST215_v1_40055) and to degrade superoxide radicals
	(identification of superoxide dismutase (EC number: 1.15.1.1; locus tags:
	COMBST215_v1_20566; 40196; 50105) and catalase enzymes (EC number:
	1.11.1.21; locus tag: COMBST215_v1_11754 and EC: 1.11.1.6; locus tags:
	COMBST215_v1_60157; 140122)). In comparison with other closely related strains,

  T to a novel species, of a novel genus, for which the name Scleromatobacter humisilvae gen. nov., sp. nov. is proposed.Scleromatobacter sp. (scle.ro′mae. N.L. gen. n. scleromae, of scleroma, a hardened part; derived from the colonies that are incrusted in solid medium when the strain grows in Petri dishes).Scleromatobacter humisilvae (hu.mi.sil'vae. L. fem. n. humus, soil; L. fem. n. silva, forest; N.L. gen. fem. n. humisilvae; from forest soil; from the forest soil where the strain has been isolated).

	Displays the following properties in addition to those given in the genus description:
	Colonies are circular, rough and incrusted in the agar medium with a color between
	white and ivory. Optimal growth occurs at 20-22°C, pH 6 and 0% NaCl. Positive for
	nitrate reduction. Does not respire chlorate. The following carbon sources are used:
	L-arabinose, D-cellobiose, D-glucose, D-ribose, D-arabitol, adonitol, butyrate,
	DESCRIPTION OF SCLEROMATOBACTER GEN. NOV. gluconate, pyruvate, L-leucine, L-proline, N-acetylglucosamine, p-hydroxy
	phenylacetic acid, bromo succinic acid, L-pyroglutamique acid, tween 40 and 80,
	Cells are Gram-negative, mesophilic, aerobic, chemoorganotrophic, straight rod-
	shaped (0.6 to 0.9 µm by 1.7 to 2.7 µm in size) and motile with presence of storage
	granules. Oxidase-negative and catalase-positive. The predominant fatty acids are
	C 16:1 ω7c, C 16:0 and C 14:0 2-OH. The polar lipid profile consists of a mixture of
	phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol and the
	main ubiquinone is Q-8. The estimated size of the genome is 6.28 Mb with a DNA
	G+C content of 69.56 mol%. Phylogenetically, on the base of whole genome
	comparisons, the genus belongs to the family Comamonadaceae, order
	Burkholderiales. Overall, the genus belongs to the Rubrivivax-Roseateles-Leptothrix-
	Azohydromonas-Aquincola-Ideonella branch. The type species is Scleromatobacter
	humisilvae (BS-T2-15 T ).

DESCRIPTION OF SCLEROMATOBACTER HUMISILVAE GEN. NOV. SP. NOV.

uridine, putrescine and dextrine. On the contrary, unable to use: citrate, acetate, aspartate, benzoate, formate, methyl-pyruvate, mono-methyl-succinate, cis-aconitic

Acknowledgements

We are grateful to Claire Geslin (UBO, LM2E) and Philippe Eliès (UBO, Plateforme d'imagerie et de mesures en microscopie (PIMM)) for their technical assistance in TEM imaging. We acknowledge Nadège Bienvenu (UBO, LM2E) for her help concerning the deposit of the strain at the UBOCC. We thank Erwann Vince and Xavier Philippon for their technical help concerning ionic chromatography. The LABGeM (CEA/Genoscope & CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform. The UMR1136 is supported by the ANR through the Labex Arbre (ANR-11-LABX-0002-01).

Funding information

This research was funded by the Sino-French IRP 1211 MicrobSea to K.A. and by the UMR6197.

Conflict of interest

The authors declare that there are no conflicts of interest.


Mélanie Save

Bertrand Guin

Anaïs Bompard

Séverine Barry

Emilie Bard

Bernard Schmitt

Isabelle Delporte

Xavier Bailly

Zouheira Djelouadji

Claire A M Becker

la diffusion de documents scientifiques de niveau

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Influence du mode de naissance et d'une complémentation en pré-et post-biotiques sur le microbiote intestinal du veau nouveau-né

OBJECTIFS◗

  Décrire les modifications du microbiote intestinal des veaux (richesse, diversité et composition) au cours de leurs 20 premiers jours de vie en fonction de leur mode de naissance et de la complémentation en ProbioactiFAP® 1 (Technologie FAP®). ◗ Évaluer l'impact d'autres facteurs liés à l'animal (parité de la mère, sexe), à la gestion de l'élevage (administration colostrum) ou à leur santé (diarrhée ou traitement antibiotique).CONCLUSIONCette étude permet de démontrer des changements importants de la composition du microbiote intestinal des veaux en fonction de leur mode de naissance : les veaux nés par césarienne ont moins de lactobacilles et d'entérobactéries, potentiellement en lien avec l'absence d'engagement dans la filière pelvienne. Nous avons aussi démontré l'effet de la complémentation en ProbioactiFAP® (Foriflor® pâte orale), en 2 jours à la naissance, qui se traduit par une augmentation significative de la richesse et de la diversité du microbiote quel que soit le mode de naissance, ces différences sont maintenues durant la phase critique des premiers jours de vie avec une proportion plus importante de lactobacilles, favorisant la digestion du lait. D'autres facteurs comme le mode d'administration du colostrum ont également un impact sur la composition du microbiote des veaux. ➤ Pas d'effet significatif du mode de vêlage sur la richesse et la diversité du microbiote à la naissance ➤ Augmentation significative de la diversité (P value = 0,049) et richesse (P value = 0,0015) du microbiote lors de la complémentation en ProbioactiFAP® ➤ Effets de la complémentation maintenus les 1 ers j de vie ➤ +6 %, +3,5% et +0,2% de diversité à J1, J5 et J10 ➤ +26,4% et +6,7% de richesse à J1 et J5 MATÉRIELS & MÉTHODES Animaux et prélèvements ◗ 27 quartets de veaux (2 nés par césarienne et 2 par voie naturelle) ont été recrutés dans 19 élevages, soit 108 veaux. ◗ Les veaux de chaque paire ont été randomisés dans deux bras d'intervention : l'un des deux a été complémenté en ProbioactiFAP® (FAP®) : Fortiflor®, seringue pâte orale, à la naissance et 24h après. ◗ En tenant compte des 6 quartets incomplets (manque du 2d veau né par césarienne ou décès du veau) nous avons obtenu quatre groupes équilibrés de 25 ou 26 veaux, soit 102 veaux. ◗ Sur chaque veau des prélèvements de fèces ont été réalisés à J1, J5, J10 et J20 pour analyse du microbiote intestinal.

➤

  Moins d'Enterobacterales à J1 ➤ Moins de Lactobacilles jusqu'à J10 ➤ Plus de Bacteroidales à J1 ➤ Moins d'Enterobacterales à J1 ➤ Plus de Lactobacilles ➤ Plus d'Enterobacterales à J1 ➤ Moins de Lactobacilles et de Bacteroidales jusqu'à J5 Séquençage de l'ADN 16S ◗ Après extraction d'ADN, la région V4-V5 du gène 16S a été amplifiée puis séquencée pour obtenir les tables d'abondance relative des unités taxonomiques opérationnelles (OTU) de chaque échantillon. Analyse statistique ◗ L'effet du mode de naissance et de la complémentation en FAP® sur la richesse et la diversité du microbiote a été évalué à l'aide d'un modèle linéaire à effet aléatoire élevage ◗ La composition du microbiote intestinal et son évolution ont été modélisées à l'aide de deux modèles de régression logistique hiérarchiques combinés sur la présence et le niveau de présence des OTU dans l'échantillon.

Étude randomisée contrôlée chez les veaux charolais LA SANTÉ DU MICROBIOTE®

	TECHNOLOGIE EXCLUSIVE ORIGINAL PROCESS
		Voie Naturelle				Voie Naturelle +FAP®				Césarienne					Césarienne +FAP®
		N=25						N=26					N=25						N=26
		1.00																							Coriobacteriales
																									Bacteroidales
		0.75																							Lactobacillales
																									Clostridiales
	Proportion de chaque Order	0.00 0.25 0.50																							Erysipelotrichales Firmicutes Veillonellales Fusobacteriaceae Burkholderiales Enterobacterales Pasteurellales
		J1 VN	J1 Cesa	J5 VN	J5 Cesa	J10 VN	J10 Cesa	J20 VN	J20 Cesa	J1 cont.	J1 FAP	J5 cont.	J5 FAP	J10 cont.	J10 Fap	J20 cont	J20 FAP	J1 Mamelle	J1 Drench	J5 Mamelle	J5 Drench	J10 Mamelle	J10 Drench	J20 Mamelle	J20 Drench
		Jour et mode de naissance			Jour et complémentation				Jour et prise colostrale
		Composition du microbiote intestinal (à l'échelle de l'ordre) en fonction du jour et des facteurs évalués

(1) ProbioactiFAP® : produits issus de la fermentation lactique de céréales Process FAP® -

Original Process Influence du mode de naissance et d'une complémentation en pré-et post-biotiques sur le microbiote intestinal du veau nouveau-né

	Mélanie SAVE 1 , Bertrand GUIN 2 , Anais BOMPARD 3 ,	1 -Clinique vétérinaire les Amognes,	5 -Original Process,
	Séverine BARRY 3 , Émilie BARD 3 , Bernard SCHMITT 4 ,	2 -Clinique vétérinaire Vet'alliance,	6 -USC 1233,
	Isabelle DELPORTE 5 , Xavier BAILLY 3 ,	3 -UMR EPIA,	7 -VetAgro Sup, département ESPV
	Zorée DJELOUADJI 6 , Claire BECKER 7 , Thibaut LURIER 3	4 -CERNh,

*auteur correspondant : thibaut.lurier@vetagro-sup.fr CONTEXTE ◗ Importance du lien entre la santé des veaux et l'implantation de leur microbiote au cours des premiers jours de leur vie. ◗ Aucune étude évaluant l'impact du mode de naissance (césarienne ou voie naturelle) sur la composition du microbiote intestinal des veaux. ◗ Peu de prébiotiques, probiotiques ou post-biotiques commercialisés pour les veaux ont été scientifiquement validés comme induisant des modifications du microbiote intestinal des veaux.

OP-F-FR-M-V-SPOS-FO-VO-JNGTV-0223Journées desGTV 2023, Poitiers, 24,25 et 26 mai 2023