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Abstract Micrarchaeota is a distinctive lineage assigned to the DPANN archaea, which includes poorly characterised microorganisms with reduced genomes that likely depend on interactions with hosts for growth and survival. Here, we report the enrichment of a stable co-culture of a member of the Micrarchaeota (Ca. Micrarchaeum harzensis) together with its Thermoplasmatales host (Ca. Scheffleriplasma hospitalis), as well as the isolation of the latter. We show that symbiont-host interactions depend on biofilm formation as evidenced by growth experiments, comparative transcriptomic analyses and electron microscopy. In addition, genomic, metabolomic, extracellular polymeric substances and lipid content analyses indicate that the Micrarchaeon symbiont relies on the acquisition of metabolites from its host. Our study of the cell biology and physiology of a Micrarchaeon and its host adds to our limited knowledge of archaeal symbioses. # Description of contents of this directory ## 1_Genomes.tar.gz Contains the protein files used for the annotations and to extract certain proteins for phylogenetic analyses. ## 2_Annotations.tar.gz This folder contains the full workflow to annotate the genomes of interest and a jupyter lab book (python3) used for parsing the data. Additionally, this folder contains: 0_Dependencies: Any custom scripts used as well as databases and mapping files (only provided if databases were modified) 1_Input: Output of the annotation workflow as well as any mapping file required by the python3 script to further parse the data 2_Output: Parsed annotation table ## 3_Phylogenies.tar.gz Contains all files generated for the phylogenies of certain lipid genes. These files are provided for the archaea only and the universal analysis (see Methods of the main paper for details). Each foldercontains: required scripts and mapping files raw sequences (protein, faa), separate for each lipid gene of interest. These come in individual versions: indiv: sequences for all arcogs final: sequences for arcogs and if several arcogs were assigned to the same COG, these arCOGs were combined into one file. If arCOGs were combined, this is listed in the provided overview table in the main directory. aligned sequences aligned and trimmed sequences output from IQ-TREE PDFs for each individual tree ## 4_raw data_ARMAN lipids Lipid extracts were analyzed by UHPLC–atmospheric pressure chemical ionization (APCI) MS for archaeal core lipids, including archaeol (diether, C20 isoprenoid chains) and glycerol dialkyl glycerol tetraether (GDGTs, tetraether, C40 side chain), according to Hopmans et al., 2016 (Organic geochemistry 93:1-6), with some modifications. Briefly, the analysis was performed on an Agilent 1260 UHPLC coupled to a 6130 quadrupole MSD in selected ion monitoring (SIM) mode. Files provided here are raw data files out of these analyses: Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract (U1808198) analysis includes the core lipid analysis of those present in the culture; Ca. Scheffleriplasma hospitalis Bligh&Dyer total lipid extract after acid hydrolysis (U1809068) includes the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run. Run U1809060 corresponds to the run of the Bligh&Dyer total lipid extract of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the present core lipids. Run U1809066, corresponds to the run of the Bligh&Dyer total lipid extract after acid hydrolysis of the co-culture of Ca. Micrarchaeum harzensis and Ca. Scheffleriplasma hospitalis, including the the intact polar-lipid-derived core lipids plus the core lipids of the previous analysis run. - Comment for Version 2: We forgot to upload files in a subfolder in 3_Phylogenies and provide them now in this updated version. - Comment for Version 3: Added some new data (4_raw data_ARMAN lipids)

After the change over from the C-wall to the ITER-like Be/W wall (ILW) in JET, the radiation losses during ICRF heating have increased and are now substantially larger than those observed with NBI at the same power levels, in spite of the similar global plasma energies reached with the two heating systems. A comparison of the NBI and ICRF performances in the JET-ILW experiments, based on a statistical analysis of ~3000 L-mode discharges, will be presented.

E. Joffrin, M. Baruzzo, M. Beurskens, Bourdelle, S. Brezinsek, J. Bucalossi, P. Buratti, G. Calabro, C.D. Challis, M. Clever, J. Coenen, E. Delabie, R. Dux, P. Lomas, E. de la Luna, P. de Vries, J. Flanagan, L. Frassinetti, D. Frigione, C. Giroud, M. Groth, N. Hawkes, J. Hobirk, M. Lehnen, G. Maddison, J. Mailloux, C.F. Maggi, G. Matthews, M. Mayoral, A. Meigs, R. Neu, I. Nunes, T. Puetterich, F. Rimini, M. Sertoli, B. Sieglin, A.C.C. Sips, G. van Rooij, I. Voitsekhovitch and JET EFDA contributors In the recent JET experimental campaigns with the new ITER-like Wall (JET-ILW), major progress has been achieved in the characterisation and operation of the H-mode regime in metallic environment: i) plasma breakdown has been achieved at the first attempt and X-point L-mode operation recovered in a few days of operation, ii) stationary and stable type I ELMy Hmodes with bN~1.4 have been achieved in low and high triangularity ITER­like shape plasmas and are showing that their operational domain at H = 1 is significantly reduced with the JET-ILW mainly because of the need to inject large amount of gas (above 1022D/s) to control core radiation. iii) in contrast the hybrid H-mode scenario has reached H factor of 1.2 to 1.3 at bN of 3 for 2 to 3s. iv) in comparison to carbon equivalent discharges, total radiation is similar but the edge radiation is lower and Zeff of the order of 1.3-1.4. At low gas fuelling rate (below 0.5 1022D/s) and low ELM frequency (typically less than 10Hz), strong core radiation peaking is observed in H-mode discharges even when tungsten influx from the divertor is constant. High Z impurity transport from the plasma edge to the core appears to be the dominant factor to explain is paper reviews the major physics and operational achievements and challenges that an ITERlike wall configuration has to face to produce stable plasma scenarios with maximised performance.

The most recent JET campaign has focused on characterizing operation with the "ITER-like" wall. One of the questions that needed to be answered is whether the auxiliary heating methods do not lead to unacceptably high levels of impurity influx, preventing fusion-relevant operation. In view of its high single pass absorption, hydrogen minority fundamental cyclotron heating in a deuterium plasma was chosen as the reference wave heating scheme in the ion cyclotron domain of frequencies. The present paper discusses the plasma behavior as a function of the minority concentration X[H] in L-mode with up to 4MW of RF power. It was found that the tungsten concentration decreases by a factor of 4 when the minority concentration is increased from X[H] 5% to X[H] 20% and that it remains at a similar level when X[H] is further increased to 30%; a monotonic decrease in Beryllium emission is simultaneously observed. The radiated power drops by a factor of 2 and reaches a minimum at X[H] 20%. It is discussed that poor single pass absorption at too high minority concentrations ultimately tailors the avoidance of the RF induced impurity influx. The edge density being different for different minority concentrations, it is argued that the impact ICRH has on the fate of heavy ions is not only a result of core (wave and transport) physics but also of edge dynamics and fueling.

R. Neu, S. Brezinsek, M. Beurskens, V. Bobkov, P. de Vries, C. Giroud, E. Joffrin, A. Kallenbach, G.F. Matthews, M.-L. Mayoral, G. Pautasso, Th. Puetterich, F. Ryter, J. Schweinzer, ASDEX Upgrade Team and JET EFDA contributors ASDEX Upgrade (AUG) has been converted to all W plasma facing components (PFCs) in 2007 and JET has implemented the ITER like wall (ILW) project (2011) using the same PFC configuration as ITER during its active phase, namely Be in the main chamber and tungsten in the divertor. As a result of the all metal PFCs in both devices much less surface conditioning is needed to arrive at reproducible wall conditions. Specifically the Be PFCs of JET led to a very small low-Z content (reduction of C and O by at least a factor of 10), reducing the edge radiation in steady state operation as well as during disruptions. Both devices successfully employ massive gas injection to mitigate disruption forces and power loads to PFCs by radiating up to 100% of the available energy. Hydrogen retention is strongly reduced (AUG: factor 5, JET: factor 10) and the remaining retention is still dominated by co-deposition with residual C in AUG and intrinsic Be in JET. The very low edge and divertor radiation could be compensated by impurity seeding either by a single gas species (N2) (AUG and JET) or by combining N2 and Ar (AUG) injection for divertor and main chamber radiation, respectively. The W sputtering in the divertor increases when seeding small amounts of N2, but decreases for higher fluxes due to the plasma cooling provided by the nitrogen radiation. The tungsten content is controlled by the source as well as by its edge and central transport. It could be kept sufficiently small by using a minimum gas fuelling to reduce the W erosion and to diminish the W penetration. The control of the central W transport by central (wave) heating had been well established in AUG, however in both devices theWcontent is increased during ICRH operation most probably due to increasedW sputtering caused by rectified sheaths. The H-Mode threshold is reduced by 20-30% in AUG and JET, but on average the confinement is lower in JET-ILW than with C PFCs. To date it is not yet clear, whether the reduced H-Mode confinement has to be attributed to the use of W PFCs, since such a clear trend as in JET was not found in AUG. The increase of confinement with N2 seeding observed in both devices hints to the fact, that low-Z impurities like carbon or nitrogen play a beneficial role for the pedestal confinement.

Migration of impurities in tokamaks has been studied with the help of tracer-injection (13C and 15N) experiments in JET and ASDEX Upgrade since 2001. We have identified a common pattern for the migrating particles: SOL flows drive impurities from the low-field side towards the high-field side of the vessel. Migration is also sensitive to the density and magnetic configuration of the plasma, and strong local variations in the resulting deposition patterns require 3D treatment of the migration process. Moreover, re-erosion of the deposited particles has to be taken into account to properly describe the migration process during steady-state operations of the reactor.

A short review of prior results on W-erosion, W-screening of the divertor and W-transport in the pedestal and the plasma core is given. The W-transport in the core plasma of JET is investigated experimentally by deriving the W-concentration profiles from modelling of the signals of the soft X-ray cameras. For the case of pure neutral beam heating W-accumulates in the core to W-concentrations of 10­3 in between the sawtooth crashes, which flatten the W-profile to a concentration of about 3¥10­5. When central ICRH heating is additionally applied the core Wconcentration decays in phases that exhibit a changed mode activity, while also the electron temperature increases and the density profile becomes less peaked. The immediate correlation between the change of MHD and the removal of W from the plasma core supports the theory that the change of the MHD activity is the underlying cause for the change of transport. Furthermore, two discharge scenarios from ASDEX Upgrade are investigated. In the first case the central W-radiation influences the core W-transport such that slowly increasing W-radiation leads to a steepening of the W-concentration profiles. In the second case two discharges are compared in which a small change of the heating trajectory leads to a change of the W-transport and a change of the sawtooth behaviour. It is speculated that the W-accumulation is the underlying reason for the irregular sawteeth, which in turn aids the W-accumulation.

The major aspects linked to the use of the JET auxiliary heating systems: NBI, ICRF and LHCD, in the new JET ITER-like wall (JET-ILW) are presented. We show that although there were issues related to the operation of each system, efficient and safe plasma heating was obtained with room for higher power. For the NBI up to 25.7MW was safely injected; issues that had to be tackled were mainly the beam shine-through and beam re-ionisation before its entrance into the plasma. For the ICRF system, 5MW were coupled in L-mode and 4MW in H-mode; the main areas of concern were RF-sheaths related heat loads and impurities production. For the LH, 2.5MW were delivered without problems; arcing and generation of fast electron beams in front of the launcher that can lead to high heat loads were the keys issues. For each system, an overview will be given of: the main modifications implemented for safe use, their compatibility with the new metallic wall, the differences in behavior compared with the previous carbon wall, with emphasis on heat loads and impurity content in the plasma.

The baseline type I ELMy H-mode scenario has been re-established in JET with the new tungsten MKII-HD divertor and beryllium on the main wall (hereafter called ITER-like wall, JET-ILW). The first JET-ILW results show that the confinement is degraded by 20­30% in the baseline scenarios compared to the previous carbon wall JET (JET-C) plasmas. The degradation is mainly driven by the reduction in the pedestal temperature. Stored energies and pedestal temperature comparable to the JET-C have been obtained in JET-ILW baseline plasmas only in the high triangularity shape using N2 seeding. This work compares the pedestal behaviour and the energy losses during ELMs in JET-ILW baseline plasmas with and without N2 seeding with similar JET-C baseline plasmas. ELMs in the JET-ILW differ from those with the carbon wall both in terms of time scales and energy losses. The ELM time scale, defined as the time to reach the minimum pedestal temperature soon after the ELM collapse, are 2ms in the JET-ILW and lower than 1ms in the JET-C. The energy losses relative to the pedestal energy are DWELM/Wped 7­12% in the JET-ILW and DWELM/Wped 10­20% in JET­C. In both cases, the energy losses fit relatively well with earlier multi machine empirical scalings of DWELM/Wped with collisionality. The time scale of the ELM collapse seems to be related to the pedestal collisionality. However, most of the non-seeded JET-ILW ELMs are followed by a further energy drop characterized by a slower time scale 10­15ms (hereafter called slow transport events), that can lead to losses in the range DWslow/Wped 15­22%, i.e. slightly larger than the JET-C ELM energy losses. On the other hand, the JET-ILW plasmas with N2 seeding have a ELM behaviour similar to the JET-C, both in terms of time scales, energy losses and absence of the slow transport events.

In both JET and ASDEX Upgrade (AUG) the plasma energy confinement has been affected by the presence of a metal wall by the requirement of increased gas-fuelling to avoid tungsten pollution of the plasma. In JET with a beryllium/tungsten wall the high triangularity baseline H-mode scenario (i.e. similar to the ITER reference scenario) has been strongest affected and the benefit of high shaping to give good normalised confinement of H98~1 at high Greenwald density fraction of fGW ~0.8 has not been recovered to date. In AUG with a full tungsten wall a good normalised confinement H98~1 could be achieved in the high triangularity baseline plasmas, albeit at elevated normalised pressure bN>2. The confinement lost with respect to the carbon devices can be largely recovered by the seeding of nitrogen in both JET and AUG. This suggests that the absence of carbon in JET and AUG with a metal wall may have affected the achievable confinement. Threemechanisms have been tested that could explain the effect of carbon or nitrogen (and the absence thereof) on the plasma confinement. First it has been seen in experiments and by means of non-linear gyrokinetic simulations (with the GENE code), that nitrogen seeding does not significantly change the core temperature profile peaking and does not affect the critical ion temperature gradient. Secondly, the dilution of the edge ion density by the injection of nitrogen is not sufficient to explain the plasma temperature and pressure rise. For this latter mechanism to explain the confinement improvement with nitrogen seeding, strongly hollow Zeff profiles would be required, which is not supported by experimental observations. The confinement improvement with nitrogen seeding cannot be explained with these two mechanisms. Thirdly, detailed pedestal structure analysis in JET high triangularity baseline plasmas have shown that fuelling of either deuterium or nitrogen widens the pressure pedestal. However, in JET-ILW this only leads to a confinement benefit in the case of nitrogen seeding where as the pedestal widens, the obtained pedestal pressure gradient is conserved. In the case of deuterium fuelling in JET-ILW the pressure gradient is strongly degraded in the fuelling scan leading to no net confinement gain due to the pedestal widening. The pedestal code EPED correctly predicts the pedestal pressure of the unseeded plasmas in JET-IW within +/­5%, however it does not capture the complex variation of pedestal width and gradient with fuelling and impurity seeding. Also it does not predict the observed increase of pedestal pressure by nitrogen seeding in JET-ILW. Ideal peeling ballooning MHD stability analysis shows that the widening of the pedestal leads to a down shift of the marginal stability boundary by only 10-20%. However, the variations in the pressure gradient observed in the JET-ILW fuelling experiment is much larger and spans a factor of more than two. As a result the experimental points move from deeply unstable to deeply stable on the stability diagram in a deuterium fuelling scan. In AUG-W nitrogen seeded plasmas, also a widening of the pedestal has been observed, consistent with the JET observations. The absence of carbon can thus affect the pedestal structure, and mainly the achieved pedestal gradient, which can be recovered by seeding nitrogen. The underlying physics mechanism is still under investigation and requires further understanding of the role of impurities on the pedestal stability and pedestal structure formation.

The change over from a full carbon to a full metal wall has reduced the accessible operational space in both AUG and JET tokamaks. The AUG carbon wall (AUG-C) was replaced in a step wise manner from 1999 to 2007 by a DEMO-relevant full W-wall and divertor (AUG-W) [1], whereas in JET the carbon wall (JET-C) was fully replaced in 2009-2010 by an ITER-like Be main chamber first wall and W divertor (JET-ILW) [2]. We have found a common pattern in these full metal devices that the global and pedestal confinement are affected by a requirement for increased gas fuelling (to screen high-Z impurities influxes). Figures 1 a&b show a comparison of Type I ELMy H-mode plasmas in AUG (Ip = 1MA, BT = 2-3T, bN = 0.2, PIn = 3-6 MW, 1.3 < bN < 1.6 ­ to be updated) [3]. The figures show that when the same density is obtained and the same fuelling level is applied the normalised confinement in terms of H98y,2 is similar between AUG-C and AUG-W. In comparison, Figure 2 shows the confinement for JET Type I ELMy H-mode plasmas (Ip = 2.4-2.6MA, BT = 2.3-2.7T, dav = 0.2 and 0.4, PNBI = 12-16MW, 1.3 < bN < 1.8). For low triangularity (d) plasmas, the downward trend of H98y,2 with density follows a similar trend as was reported for JET-C in [4] and is in agreement with the AUG observations. However, for the high-d plasmas a further degradation is observed; whereas in JET-C high d plasmas could sustain good confinement H98y,2~1 up to the Greenwald density limit, the benefit of d seems to have disappeared in JET-ILW [5,6].

The baseline type I ELMy H-mode scenario has been re-established in JET with the new tungsten MKII-HD divertor and beryllium-main wall (hereafter called ITER-like wall, ILW). In general, the confinement in the ILW plasmas tends to be lower than in the corresponding carbon fibre composite (CFC) wall plasmas, mainly due to a reduction in the pedestal temperature. A partial recovery to a pedestal pressure comparable to the CFC case has been obtained in high triangularity plasmas with N2 seeding. The aim of this work is to compare the ELM behaviour in JET with the CFC wall and with the ILW in order to shed light on the confinement differences. The work will focus on the electron temperature (Te) and density (Ne), on the stored energy and on the ELM time scale.

G.P. Maddison, C. Giroud, B. Alper, G. Arnoux, I. Balboa, M.N.A. Beurskens, A. Boboc, S. Brezinsek, M. Brix, M. Clever, R. Coelho, J.W. Coenen, I. Coffey, P.C. da Silva Aresta Belo, S. Devaux, P. Devynck, T. Eich , R.C. Felton, J. Flanagan, L. Frassinetti, L. Garzotti, M. Groth, S. Jachmich, A. Järvinen, E. Joffrin, M.A.H. Kempenaars, U. Kruezi , K.D. Lawson, M. Lehnen, M.J. Leyland, Y. Liu, P.J. Lomas, C.G. Lowry, S. Marsen, G.F. Matthews, G.K. McCormick, A.G. Meigs, A.W. Morris, R. Neu, I.M. Nunes, M. Oberkofler, F.G. Rimini, S. Saarelma, B. Sieglin, A.C.C. Sips, A. Sirinelli , M.F. Stamp , G.J. van Rooij, D.J. Ward , M. Wischmeier and JET EFDA contributors The former all-carbon wall on JET has been replaced with beryllium in the main torus and tungsten in the divertor to mimic the surface materials envisaged for ITER. Comparisons are presented between Type I H-mode characteristics in each design by examining respective scans over deuterium fuelling and impurity seeding, required to ameliorate exhaust loads both in JET at full capability and in ITER. Attention is focused upon a common high-triangularity, single-null divertor configuration at 2.5MA, q95 3.5 yielding the most robust all-C performance. Contrasting results between the alternative linings are found firstly in unseeded plasmas, for which purity is improved and intrinsic radiation reduced in the ITER-like wall (ILW) but normalised energy confinement is 30% lower than in all-C counterparts, owing to a commensurately lower (electron) pedestal temperature. Divertor recycling is also radically altered, with slower, inboard-outboard asymmetric transients at ELMs and spontaneous oscillations in between them. Secondly, nitrogen seeding elicits opposite responses in the ILW to all-C experience, tending to raise plasma density, reduce ELM frequency, and above all to recover (electron) pedestal pressure, hence global confinement, almost back to previous levels. A hitherto unrecognised role of light impurities in pedestal stability and dynamics is consequently suggested. Thirdly, while heat loads on the divertor outboard target between ELMs are successfully reduced in proportion to the radiative cooling and ELM recurrence effects of N in both wall environments, more surprisingly, average power ejected by ELMs and estimated scrape-off-layer pressure ratio during the approach to outboard detachment also both decline in the same proportion for the ILW. Finally, inter-ELM W sources in the ILW divertor tend to fall with N input, although core accumulation possibly due to net ELM erosion still leads to significantly less steady conditions than in all-C plasmas. This limitation of ILW H-modes so far will be readdressed in future campaigns to continue progress towards a fully-integrated scenario suitable for D-T experiments on JET and for "baseline" operation on ITER. The diverse changes in behaviour between all-C and ILW contexts demonstrate essentially the strong impact which boundary conditions and intrinsic impurities can have on tokamak-plasma states.

During the initial operation of the JET ITER-like wall, particular attention was given to the characterization of the Ion Cyclotron Resonance Frequency (ICRF) heating in this new metallic environment. In this contribution we compare L-modes plasmas heated by ICRF or by Neutral Beam Injection (NBI). ICRF heating as expected led to a much higher centrally peaked power deposition on the electrons and due to the central fast ion population to stronger sawtooth activity. Surprisingly, although a higher bulk radiation was observed during the ICRF phase, the thermal plasma energy was found similar for both cases, showing that a higher radiation inside the separatrix was not incompatible with an efficient central heating scheme. The higher radiation was attributed to the presence Tungsten (W). Tomographic inversion of SXR emissions allowed a precise observation of the sawtooth effect on the radiation pattern. W concentration profiles deconvolved from SXR emission showed the flattening of the profiles due to sawtooth for both heating and the peaking of the profiles in the NBI case only hinting for extra transport effect in the ICRF case.