1 SUPPLEMENTARY TABLES 2 3 FINE-SCALE ADAPTATIONS TO ENVIRONMENTAL VARIATION AND GROWTH 4 STRATEGIES DRIVE PHYLLOSPHERE DIVERSITY. 5 6 Jean-Baptiste Leducq1,2,3, Émilie Seyer-Lamontagne1, Domitille Condrain-Morel2, Geneviève 7 Bourret2, David Sneddon3, James A. Foster3, Christopher J. Marx3, Jack M. Sullivan3, B. Jesse 8 Shapiro1,4 & Steven W. Kembel2 9 10 1 - Université de Montréal 11 2 - Université du Québec à Montréal 12 3 – University of Idaho 13 4 – McGill University 14

1 15 Table S1 - List of reference genomes from which the complete rpoB 16 and sucA nucleotide sequences were available. Following information is shown: strain name, 17 given genus name ( considered as Methylobacterium in this study), given 18 name (when available), biome where the strain was isolated from (when available; only indicated 19 for Methylobacterium), groups (B,C) or clade (A1-A9) assignation, and references or source 20 (NCBI bioproject) when unpublished. Complete and draft Methylobacteriaceae genomes publicly 21 available in September 2020, including 153 Methylobacteria, 30 and 2 Enterovirga, 22 using blast of the rpoB complete sequence from the M. extorquens strain TK001 against NCBI 23 databases refseq_genomes and refseq_rna (1) available for Methylobacteriaceae 24 (Uncultured/environmental samples excluded)

STRAIN Genus Species ENVIRONMENT Group/ Reference/source Clade BTF04 Methylobacterium sp. Water A1 (2) Gh-105 Methylobacterium gossipiicola Phyllosphere A1 (3) GV094 Methylobacterium sp. Rhizhosphere A1 https://www.ncbi.nlm.nih.gov/bioproject /443353 GV104 Methylobacterium sp. Rhizhosphere A1 https://www.ncbi.nlm.nih.gov/bioproject /443354 Leaf100 Methylobacterium sp. Phyllosphere A1 (4) Leaf102 Methylobacterium sp. Phyllosphere A1 (4) Leaf104 Methylobacterium sp. Phyllosphere A1 (4) Leaf111 Methylobacterium sp. Phyllosphere A1 (4) Leaf112 Methylobacterium sp. Phyllosphere A1 (4) Leaf113 Methylobacterium sp. Phyllosphere A1 (4) Leaf117 Methylobacterium sp. Phyllosphere A1 (4) Leaf125 Methylobacterium sp. Phyllosphere A1 (4) Leaf465 Methylobacterium sp. Phyllosphere A1 (4) Leaf469 Methylobacterium sp. Phyllosphere A1 (4) Leaf87 Methylobacterium sp. Phyllosphere A1 (4) Leaf88 Methylobacterium sp. Phyllosphere A1 (4) Leaf89 Methylobacterium sp. Phyllosphere A1 (4) Leaf94 Methylobacterium sp. Phyllosphere A1 (4) Leaf99 Methylobacterium sp. Phyllosphere A1 (4) V23 Methylobacterium sp. Water A1 (5) WL69 Methylobacterium sp. Phyllosphere A1 (6) 10 Methylobacterium sp. Water A2 https://www.ncbi.nlm.nih.gov/bioproject /195835 77 Methylobacterium sp. Water A2 https://www.ncbi.nlm.nih.gov/bioproject /165569 88A Methylobacterium sp. Water A2 https://www.ncbi.nlm.nih.gov/bioproject /165571 Leaf106 Methylobacterium sp. Phyllosphere A2 (4) Leaf85 Methylobacterium sp. Phyllosphere A2 (4) Leaf86 Methylobacterium sp. Phyllosphere A2 (4) Leaf91 Methylobacterium sp. Phyllosphere A2 (4) Leaf93 Methylobacterium sp. Phyllosphere A2 (4) WL19 Methylobacterium sp. Phyllosphere A2 (6) Leaf108 Methylobacterium sp. Phyllosphere A3 (4) Leaf399 Methylobacterium sp. Phyllosphere A3 (4) Leaf466 Methylobacterium sp. Phyllosphere A3 (4) DSM24105 Methylobacterium brachythecii Phyllosphere A4 (7)

2 NBRC107714 Methylobacterium haplocladii Phyllosphere A4 (7) NBRC107716 Methylobacterium gnaphalii Phyllosphere A4 (8) WL9 Methylobacterium sp. Phyllosphere A4 (6) 17J42-1 Methylobacterium segetis Soil A5 (9) 17SD2-17 Methylobacterium durans Anthropo/Soil A5 (10) NBRC107715 Methylobacterium oxalidis Phyllosphere A5 (11) YIM132548 Methylobacterium planium Lichen A5 (12) YIM48816 Soil A5 (13) WL103 Methylobacterium sp. Phyllosphere A6 (6) WL116 Methylobacterium sp. Phyllosphere A6 (6) WL119 Methylobacterium sp. Phyllosphere A6 (6) WL12 Methylobacterium sp. Phyllosphere A6 (6) WL120 Methylobacterium sp. Phyllosphere A6 (6) WL30 Methylobacterium sp. Phyllosphere A6 (6) WL6 Methylobacterium sp. Phyllosphere A6 (6) WL8 Methylobacterium sp. Phyllosphere A6 (6) WL93 Methylobacterium sp. Phyllosphere A6 (6) 17Sr1-43 Methylobacterium sp. Anthropo/Soil A7 (14) CCH5-D2 Methylobacterium sp. Anthropo/Water A7 (15) SB0023/3 Methylobacterium symbioticum Fungus A8 (16) SW08-7 Methylobacterium dankookense Anthropo/Water A8 (17) 111MFTsu3.1M4 Methylobacterium brachiatum Plant A9 (18) 13MFTsu3.1M2 Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /351394 190mf Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /350406 275MFSha3.1 Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /347448 285MFTsu5.1 Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /187943 2A Methylobacterium sp. Rhizhosphere A9 (19) ARG-1 Methylobacterium sp. Fungus A9 (20) B1 Methylobacterium sp. Phyllosphere A9 (21) B34 Methylobacterium sp. Phyllosphere A9 (21) BK227 Methylobacterium sp. Endophyte A9 https://www.ncbi.nlm.nih.gov/bioproject /520059 BL36 Methylobacterium pseudosasicola Phyllosphere A9 (22) BL47 Methylobacterium phyllostachyos Phyllosphere A9 (22) C1 Methylobacterium sp. Anthropo/Water A9 (23) CBMB20 Phyllosphere A9 (24) CBMB27 Methylobacterium phyllosphaerae Phyllosphere A9 (25) DSM5686 Methylobacterium fujisawaense Unknown A9 (26, 27) DSM760 Methylobacterium organophilum Water A9 (27, 28) ES_PA-B5 Methylobacterium radiotolerans Rhizhosphere A9 https://www.ncbi.nlm.nih.gov/bioproject /PRJNA460942 GXF4 Methylobacterium sp. Endophyte A9 (29) GXS13 Methylobacterium sp. Endophyte A9 (30) JCM2831 Methylobacterium radiotolerans Seed A9 (31) = NBRC15690 Leaf361 Methylobacterium sp. Phyllosphere A9 (4) MAMP4754 Methylobacterium radiotolerans Endophyte A9 (32) ME94 Methylobacterium radiotolerans Endophyte A9 (33) P1-11 Methylobacterium sp. Rhizhosphere A9 (34) RE1.2 Methylobacterium radiotolerans Seed A9 https://www.ncbi.nlm.nih.gov/bioproject /278124 SR1.6/6 Methylobacterium mesophilicum Phyllosphere A9 (35) TX0642 Methylobacterium brachiatum Anthropo A9 (36) UNC300MFChir4. Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject 1 /351052

3 UNC378MF Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /248486 UNCCL110 Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /234870 UNCCL125 Methylobacterium sp. Plant A9 https://www.ncbi.nlm.nih.gov/bioproject /PRJNA248500 WL1 Methylobacterium sp. Phyllosphere A9 (6) WL18 Methylobacterium sp. Phyllosphere A9 (6) WL2 Methylobacterium sp. Phyllosphere A9 (6) WL64 Methylobacterium sp. Phyllosphere A9 (6) WL7 Methylobacterium sp. Phyllosphere A9 (6) XJLW Methylobacterium sp. Anthropo/Water A9 (37) YL-MPn5-2016 Methylobacterium sp. Water A9 https://www.ncbi.nlm.nih.gov/bioproject /618225 YL-MPn6-2016 Methylobacterium sp. Water A9 https://www.ncbi.nlm.nih.gov/bioproject /618226 yr668 Methylobacterium sp. Rhizhosphere A9 https://www.ncbi.nlm.nih.gov/bioproject /303324 AM1 Methylobacterium extorquens Anthropo B (38) AMS5 Methylobacterium sp. Phyllosphere B (39) B4 Methylobacterium sp. Anthropo/Water B https://www.ncbi.nlm.nih.gov/bioproject /368293 BJ001 Methylobacterium populi Endophyte B (31) CD11_7 Methylobacterium populi Anthropo/Microbio B (40) me CGMCC1.6474 Methylobacterium salsuginis Ocean B (41) CLZ Methylobacterium sp. Soil B (42) CM4 Methylobacterium extorquens Anthropo/Soil B (31) CP3 Methylobacterium extorquens Seed B (43) DB1607 Methylobacterium sp. Anthropo B https://www.ncbi.nlm.nih.gov/bioproject /495120 DM1 Methylobacterium sp. Anthropo B (44) DM4 Methylobacterium extorquens Anthropo/Water B (38) DSM11490 Methylobacterium thiocyanatum Rhizhosphere B (27, 45) DSM13060 Methylobacterium extorquens Phyllosphere B (46) DSM2163 Methylobacterium rhodinum Soil B (27, 47) DSM5687 Methylobacterium rhodesianum Anthropo B (26, 27) L1A1 Methylobacterium sp. Water B (48) Leaf123 Methylobacterium sp. Phyllosphere B (4) Leaf456 Methylobacterium sp. Phyllosphere B (4) MB200 Methylobacterium sp. Anthropo B (49) NBRC15911 Methylobacterium extorquens Anthropo B https://www.ncbi.nlm.nih.gov/bioproject /PRJDB6075 NI91 Methylobacterium sp. Soil B (42) P-1M Methylobacterium populi Anthropo/Water B (50) PA1 Methylobacterium extorquens Phyllosphere B (31) PinkelPinkel_01 Methylobacterium populi Anthropo/Soil B (51) PSBB040 Methylobacterium extorquens Water B https://www.ncbi.nlm.nih.gov/biosampl e/SAMN06210717 PSBB041 Methylobacterium zatmanii Water B https://www.ncbi.nlm.nih.gov/bioproject /PRJNA376590 Q1 Methylobacterium sp. Endophyte B https://www.ncbi.nlm.nih.gov/bioproject /529698 R2-1 Methylobacterium sp. Unknown B https://www.ncbi.nlm.nih.gov/biosampl e/SAMN12024188/ RAS18 Methylobacterium sp. Phyllosphere B (52) TK0001 Methylobacterium extorquens Soil B (53) YC-XJ1 Methylobacterium populi Unknown B (54) 174MFSha1.1 Methylobacterium sp. Plant C https://www.ncbi.nlm.nih.gov/bioproject /248487 17Sr1-1 Methylobacterium sp. Soil C https://www.ncbi.nlm.nih.gov/nuccore/1 393188502 17Sr1-28 Methylobacterium terrae Anthropo/Soil C (55)

4 17Sr1-39 Methylobacterium terricola Soil C (56) 4-46 Methylobacterium sp. Rhizhosphere C (31) 6HR-1 Methylobacterium nonmethylotrophicum Anthropo/Soil C (57) ap11 Methylobacterium sp. Rhizhosphere C https://www.ncbi.nlm.nih.gov/bioproject /303350 DB0501 Methylobacterium sp. Anthropo C https://www.ncbi.nlm.nih.gov/bioproject /606480 DSM16371 Methylobacterium aquaticum Anthropo/Water C (58) =GR16 DSM16961 Methylobacterium variabile Anthropo/Water C (59) DSM25844 Methylobacterium tarhaniae Soil C (60) JCM14648 Methylobacterium platani Phyllosphere C (61) MA-22A Methylobacterium aquaticum Phyllosphere C (62) MIMD6 Methylobacterium crusticola Soil C (63) NS228 Methylobacterium indicum Seed C Midha et al. (2016) NS229 Methylobacterium indicum Seed C Midha et al. (2016) NS230 Methylobacterium indicum Seed C Midha et al. (2016) ORS2060 Methylobacterium nodulans Rhizhosphere C (31) PMB02 Methylobacterium platani Phyllosphere C (61) PR1016A Methylobacterium currus Anthropo C (64) SE2.11 Methylobacterium platani Seed C (65) SE3.6 Methylobacterium platani Seed C (65) TER-1 Methylobacterium sp. Anthropo/Water C (66) WSM2598 Methylobacterium sp. Rhizhosphere C (67) yr596 Methylobacterium sp. Rhizhosphere C https://www.ncbi.nlm.nih.gov/bioproject /PRJNA303325 DB1703 Enterovirga sp. - - www.ncbi.nlm.nih.gov/bioproject/PRJN A224116 DSM25903 Enterovirga rhinocerotis - - (68) 17mud1-3 Microvirga sp. - - PRJNA433161 AT3.9 - - PRJNA546671 ATCCBAA-817 Microvirga flocculans - - PRJNA204104 BR3299 Microvirga vignae - - PRJNA283551 BSC39 Microvirga sp. - - PRJNA257288 c23x22 Microvirga sp. - - PRJNA613872 c27j1 Microvirga sp. - - PRJNA478116 CCBAU65841 Microvirga sp. - - PRJNA451539 CDVBN77 Microvirga sp. - - PRJNA543229 CGMCC1.7666 Microvirga guangxiensis - - PRJEB15809 DSM14364 - - PRJNA456033 DSM15743 Microvirga flocculans - - PRJNA583293 DSM21344 Microvirga aerophila - - PRJNA478467 HR1 Microvirga sp. - - PRJNA578616 JC119 Microvirga massiliensis - - PRJEA82707 KCTC23863 Microvirga makkahensis - - PRJNA597827 KLBC81 Microvirga sp. - - PRJNA451250 Lmie10 Microvirga tunisiensis - - PRJNA558675 M8 Microvirga sp. - - PRJNA558674 Marseille-Q2068 Microvirga sp. - - PRJNA646450 MGYG-HGUT- Microvirga massiliensis - - PRJEB33885 02310 NBRC106136 Microvirga aerophila - - PRJDB6229 NCCP-1258 Microvirga pakistanensis - - PRJNA529055 R24825 Microvirga sp. - - PRJNA224116 R24845 Microvirga sp. - - PRJNA224116 SYSUG3D203 Microvirga sp. - - PRJNA597795 SYSUG3D207 Microvirga sp. - - PRJNA597796 V5/3m Microvirga ossetica - - (69) WSM3557 Microvirga lotononidis - - PRJNA65303

5 25 26

6 27 Table S2 - Description of sampling sites. Following information is shown: year of sampling, 28 forest of origin (MSH: Mont Saint-Hilaire; SBL: Station Biologique des Laurentides) and plots 29 within forests, plot GPS coordinates, plot approximate elevation and list of dominant tree species 30 with number of trees sampled per species (legend below the table): ABBA (Abies balsamea), 31 ACRU (Acer rubrum). ACSA (Acer saccharum), OSVI (Ostrya virginiana), QURU (Quercus 32 rubra), FAGR (Fagus grandifolia), ASPE (Acer Pennsylvanicum).

Elevation Year Forest-plot N W ACPE ACSA ACRU FAGR OSVI QURU ABBA BEPA BEAL (m) MSH-H0 45°32'29" 73°9'47" 217 3 3 - 3 1 † - - † 2017* MSH-L0 45°32'34" 73°9'22" 175 3 3 - 3 - † - - † MSH-01 45°32'23" 73°9'28" 190 - 3 - 4 - - - - - MSH-02 45°32'28" 73°9'40" 225 - 6 - - - † - - † MSH-03 45°32'28" 73°9'50" 267 - 6 - - - † - - † MSH-04 45°32'30" 73°9'59" 288 - 2 - - 2 3 - - - MSH-05 45°32'36" 73°10'8" 315 - 3 - - 2 2 - - - 2018** MSH-06 45°32'20" 73°9'18" 170 - - - 7 - - - - - SBL-01 45°59'21" 74°0'12" 366 2 2 2 2 - - 2 † - SBL-02 45°59'30" 73°59'55" 381 2 2 2 2 - - 2 † - SBL-03 45°59'40" 73°59'20" 367 3 1 3 - - - 3 † - SBL-04 45°59'34" 73°59'29" 346 - - 5 1 - - 4 † - * Pilot survey for isolation only **Timeline survey for isolation and community analysis † abundant but no canopy below 5 meters 33 34

7 35 Table S3 - Description of trees monitored in 2018 and sample usage. The following 36 information is shown: forest, plot within forest, tree ID, tree species (ABBA: Abies balsamea, 37 ACRU: Acer rubrum, ACSA: Acer saccharum, OSVI: Ostrya virginiana, QURU: Quercus 38 rubra, FAGR: Fagus grandifolia, ASPE: Acer Pennsylvanicum), dates of sampling and use of 39 sample(s) for this date: 16S barcoding (S); rpoB barcoding (R); isolation (number of isolates 40 indicated in parenthesis).

Forest Plot Tree Species Date 1 Date 2 Date 3 Date 4 MSH 27-Jun 6-Aug 7-Sep 18-Oct 1 1 FAGR R(2) R(2) R(3) R(5) 2 FAGR R(1) R R R 3 ACSA (7) RS(1) RS(1) RS(1) 4 ACSA R(5) R R R 5 FAGR S(4) RS R RS 2 1 ACSA R R R R 4 ACSA R R R R 6 ACSA - R R R 3 1 ACSA (6) R(1) RR(1) R(0) 2 ACSA (3) R - - 3 ACSA (2) R R R 4 1 OSVI R(2) R R R 2 ACSA RS(6) RS RS RS 3 ACSA R(3) R R R 4 OSVI RS(6) RS RS RS 5 QURU R(2) - R R 6 QURU S(1) RS RS R 7 QURU (2) - - R 5 1 QURU - - R R 2 ACSA - R R R 3 ACSA - R R R 4 QURU - R R R 5 OSVI - R R R 7 OSVI - R R R 6 2 FAGR - R R R 4 FAGR - R R R 6 FAGR - (4) R(1) R(1) SBL 20-Jun 16-Jul 16-Aug 20-Sep 1 2 FAGR RS(4) RS(8) RRS(3) RS(3) 3 ACRU RS R(1) S RS 4 ACRU - - R R 7 ACPE RS RS(1) RS RS 10 ABBA RS RS(5) RS RS 2 1 ACPE R RR(0) R R 2 ACRU R R(0) R R 3 FAGR R R(2) R R 4 ACSA R(0) R(4) (1) R(2) 5 ACPE R R R R 6 ABBA R R(2) R R 3 1 ACRU R R R R 3 ABBA RS RS(3) RS RS 5 ACPE R R R R 7 ACSA RS(4) R(6) RS(2) RRS(3) 8 ACRU S RS(1) RS RS 9 ABBA R R R R 10 ACPE RS R(6) RS RS 4 1 ABBA R R R R 3 FAGR (2) R(5) R(6) R(9) 4 ABBA R R(4) R R 6 ABBA R R R R 7 ACRU - R(7) R R 8 ACRU R R - R 9 ACRU R R R R 10 ABBA R R R R

8 41 Table S4 - Summary of 16S ASV taxonomic assignation using SILVA (v.138). For each 42 taxon, the following information is shown: the number of ASVs and the average relative 43 abundance of their sequences (F), both in phyllosphere samples (n=46) and one positive control 44 (METH community). Bacterial phyllosphere diversity was assessed through Illumina sequencing 45 of the 16S RNA ribosomal gene using primer 799 F-1115R targeting the V5-V6 region and 46 excluding chloroplastic DNA (70). was assessed with emphasize on 47 Methylobacterium, hence limiting taxonomic assignation at the genus level within 48 Methylobacteriaceae, at the family level within Rhizobiales, at the order level within 49 , at the class level within , and at the phylum level within 50 . We used SILVA v.138 (71) as a database with assignTaxonomy function in R package 51 dada2 (72).

Phyllosphere METH community SILVA annotation (Blastn currations) samples ASVs F ASVs F All ASVs Bacteria 725 100.00% 24 100.00% Abditibacteriota 9 0.66% - - Acidobacteriota 24 1.76% - - Actinobacteriota 232 36.33% - - Armatimonadota 3 0.06% - - Bacteroidota 98 22.09% - - Bdellovibrionota 2 0.06% - - Chloroflexi 28 0.79% - - Cyanobacteria 1 0.21% - - Bacteria Deinococcota 28 5.67% - - Firmicutes 16 0.45% 1 0.12% Fusobacteriota 1 0.00% - - Gemmatimonadota 1 0.01% - - Myxococcota 6 0.46% - - Patescibacteria 26 1.68% - - Thermotogota - - 3 36.80% unknown 1 0.01% - - Proteobacteria 249 29.75% 20 63.08% Gammaproteobacteria 87 9.07% 3 19.22% Proteobacteria Alphaproteobacteria 162 20.69% 17 43.86% Acetobacterales 54 5.31% - - Caedibacterales 1 0.01% - - Caulobacterales 3 0.27% - - Alphaproteobacteria Rickettsiales 8 0.27% - - Sphingomonadales 23 1.61% 1 5.68% unknown 1 0.13% - - Rhizobiales 72 13.08% 16 38.18% Rhizobiaceae 3 0.03% - - Rhizobiales Xanthobacteraceae 2 0.05% - - Beijerinckiaceae* 67 12.99% 16 38.18% unknown unknown 5 0.21% - - Methylocella 4 0.50% - - (Beijerinckiaceae) Beijerinckiaceae* Methylorosula 3 1.47% - - (Lichenibacteriaceae) 1174-901-12 38 9.49% - - (Roseiarcaceae) Roseiarcus 1 0.01% - -

9 Psychroglaciecola 1 0.02% - - (Methylobacteriaceae) Methylobacterium- 15 1.29% 16 38.18% Methylorubrum A1 3 0.13% 5 14.50% A9 9 0.87% 7 16.38% Methylobacterium-Methylorubrum A6 1 0.29% 2 2.68% A10 (M. komagatae) 2 0.00% 2 4.62% 52 53

10 54 Table S5 - PERMANOVA analysis of variance in bacterial community diversity assessed 55 from 16S barcoding in 46 phyllosphere samples (10,000 permutations on ASV relative 56 abundance, Hellinger transformation). Significance of factors and interactions: “***”: p<0.00l; 57 “**”: p<0.01; “*”: p<0.05. Factor Df SumsOfSqs MeanSqs F.Model R2 Pr(>F) Forest of origin (F) 1 2.68 2.68 27.49 0.316*** 0.000 Host tree specie (H) 6 1.32 0.22 2.26 0.156*** 0.001 Time of sampling (D) 6 1.01 0.17 1.73 0.120* 0.016 F:H 1 0.17 0.17 1.77 0.020 0.080 H:D 18 2.02 0.11 1.15 0.239 0.217 Residuals 13 1.27 0.10 - 0.150 - Total 45 8.48 - - 1.000 - 58 59

11 60 Table S6 - List of 76 isolates from MSH (pilot survey in august 2017). Methylobacterium was 61 isolated on solid MMS media with 0.1% methanol and 50mg/L of Cycloheximide to reduce 62 fungal contamination (73), from 57 samples from 19 trees in two plots (H0 and L0; 9-10 trees per 63 plots samples). For each sample, isolation was duplicated at 20 and 30 °C. Isolate identification 64 was assessed by PCR amplification and sequencing of the V4 region from 16S RNA ribosomal 65 gene using primers 515F (74) and 786R (75), and then of the V4-16S sequence against NCBI 66 databases (1) refseq_genomes and refseq_rna available for Methylobacteriaceae 67 (Uncultured/environmental samples excluded). Type strains correspond to eight unique 16s 68 variants identified (isolates for which partial rpoB and sucA sequences were also amplified; 69 Table S7). Clade assignation was assessed from species names in 100% match from blast of the 70 16s sequence (blast 16S) and refined from the phylogenetic position of the type strains in rpoB 71 and sucA phylogenies (phylogeny rpoB/sucA; Figure S5). Isolates indicated in bold (†) were 72 used to build the METH community.

Temp. of Clade Tree Tree Type Plot Rep. isolation Isolate Clade (blast 16S) (phylogeny Species ID strain (°C) rpoB/sucA) H0 ACSA 1 A 30 DNA006 † DNA001 A1/A2/A3 A1 H0 ACSA 1 A 30 DNA009 DNA001 A1/A2/A3 A1 H0 ACSA 1 A 30 LYS095 DNA001 A1/A2/A3 A1 H0 ACSA 1 C 20 DNA001 DNA001 A1/A2/A3 A1 H0 ACSA 1 C 20 DNA003 DNA001 A1/A2/A3 A1 H0 ACSA 1 C 30 DNA021 † DNA021 A10 A10 H0 ACSA 1 C 30 LYS086 DNA021 A10 A10 H0 ACSA 2 A 30 LYS091 DNA021 A10 A10 H0 ACSA 2 C 20 DNA014 DNA001 A1/A2/A3 A1 H0 ACSA 2 C 20 DNA022 † - Sphingomonas - H0 ACSA 3 C 30 LYS030 - Stenotrophomonas - H0 ACPE 4 C 30 DNA016 DNA001 A1/A2/A3 A1 H0 ACPE 5 A 30 DNA008 LYS069 A1/A2/A3 A2 H0 ACPE 5 A 30 LYS093 LYS069 A1/A2/A3 A2 H0 ACPE 5 C 20 LYS055 DNA007 A6 A6 H0 ACPE 5 C 20 LYS056 DNA007 A6 A6 H0 ACPE 5 C 20 LYS059 DNA007 A6 A6 H0 ACPE 5 C 30 DNA005 DNA011 A9 A9 H0 ACPE 5 C 30 DNA019 DNA001 A1/A2/A3 A1 H0 ACPE 6 A 30 LYS081 DNA021 A10 A10 H0 ACPE 6 B 20 DNA024 † DNA001 A1/A2/A3 A1 H0 ACPE 6 B 20 LYS057 DNA001 A1/A2/A3 A1 H0 ACPE 6 B 20 LYS058 DNA007 A6 A6 H0 FAGR 7 A 30 LYS028 DNA001 A1/A2/A3 A1 H0 FAGR 7 C 20 LYS076 DNA001 A1/A2/A3 A1 H0 FAGR 7 C 30 LYS047 DNA021 A10 A10 H0 FAGR 7 C 30 LYS090 DNA021 A10 A10 H0 FAGR 8 A 30 LYS039 DNA001 A1/A2/A3 A1 H0 FAGR 8 B 30 LYS031 DNA001 A1/A2/A3 A1 H0 FAGR 8 C 30 LYS096 DNA001 A1/A2/A3 A1 H0 FAGR 9 C 20 LYS060 DNA001 A1/A2/A3 A1 H0 FAGR 9 C 20 LYS061 DNA007 A6 A6

12 H0 FAGR 9 C 20 LYS072 DNA011 A9 A9 H0 FAGR 9 C 20 LYS075 DNA007 A6 A6 H0 OSVI 10 B 20 DNA013 † DNA013 A6 A6 H0 OSVI 10 B 20 DNA018 † DNA018 A1/A2/A3 A1 H0 OSVI 10 B 20 DNA023 DNA007 A6 A6 H0 OSVI 10 B 20 LYS032 DNA007 A6 A6 H0 OSVI 10 B 20 LYS033 DNA007 A6 A6 H0 OSVI 10 B 20 LYS035 DNA007 A6 A6 H0 OSVI 10 B 20 LYS036 DNA011 A9 A9 H0 OSVI 10 B 20 LYS037 DNA007 A6 A6 H0 OSVI 10 B 20 LYS043 DNA001 A1/A2/A3 A1 H0 OSVI 10 B 20 LYS051 DNA001 A1/A2/A3 A1 H0 OSVI 10 B 20 LYS052 DNA007 A6 A6 H0 OSVI 10 B 20 LYS053 DNA007 A6 A6 L0 ACSA 1 A 30 LYS080 DNA011 A9 A9 L0 ACSA 1 A 30 LYS082 LYS069 A1/A2/A3 A2 L0 ACSA 1 C 20 LYS067 DNA011 A9 A9 L0 ACSA 1 C 20 LYS068 DNA001 A1/A2/A3 A1 L0 ACSA 1 C 30 DNA010 † DNA001 A1/A2/A3 A1 L0 ACSA 1 C 30 DNA011 DNA011 A9 A9 L0 ACSA 2 A 30 DNA004 DNA011 A9 A9 L0 ACSA 2 C 20 LYS069 LYS069 A1/A2/A3 A2 L0 ACSA 2 C 30 LYS083 DNA001 A1/A2/A3 A1 L0 ACSA 2 C 30 LYS094 DNA001 A1/A2/A3 A1 L0 ACSA 3 A 20 LYS070 DNA001 A1/A2/A3 A1 L0 ACSA 3 A 20 LYS071 - Sphingomonas - L0 ACSA 3 A 30 LYS089 DNA001 A1/A2/A3 A1 L0 ACPE 4 B 30 LYS084 DNA011 A9 A9 L0 ACPE 5 C 30 LYS041 DNA011 A9 A9 L0 ACPE 6 A 20 LYS054 DNA001 A1/A2/A3 A1 L0 ACPE 6 B 30 LYS078 DNA021 A10 A10 L0 FAGR 7 A 30 LYS046 DNA021 A10 A10 L0 FAGR 7 A 30 LYS077 DNA001 A1/A2/A3 A1 L0 FAGR 7 B 30 LYS025 DNA011 A9 A9 L0 FAGR 7 B 30 LYS049 DNA021 A10 A10 L0 FAGR 7 B 30 LYS050 DNA021 A10 A10 L0 FAGR 7 C 20 LYS062 DNA007 A6 A6 L0 FAGR 7 C 30 LYS027 DNA001 A1/A2/A3 A1 L0 FAGR 8 B 30 LYS088 DNA021 A10 A10 L0 FAGR 8 C 20 DNA007 † DNA007 A6 A6 L0 FAGR 8 C 20 DNA020 † DNA020 A10 A10 L0 FAGR 8 C 20 LYS038 DNA001 A1/A2/A3 A1 L0 FAGR 8 C 20 LYS065 DNA007 A6 A6 L0 FAGR 8 C 20 LYS066 DNA007 A6 A6 L0 FAGR 8 C 30 LYS085 DNA001 A1/A2/A3 A1 L0 FAGR 9 C 20 LYS064 - Deinococcus - L0 FAGR 9 C 20 DNA012 † DNA011 A9 A9 L0 FAGR 9 C 20 LYS063 DNA007 A6 A6 73 74

13 75 Table S7 - Primers used to amplify hyper variable regions in genes sucA and rpoB. Sequence 76 amplification success (%) in 20 Methylobacterium isolates from a pilot survey in MSH in august 77 2017 (see Table S6). These genes were used as an alternative to the 16S rRNA gene to develop a 78 highly polymorphic marker targeting specifically the Methylobacteriaceae family. For each of 79 the five hyper variable regions (three in sucA, two in rpoB), primers were designed in flanking by 80 well-conserved regions.

Clade A1 A2 A6 A9 A10 DNA001 DNA006 DNA010 DNA011 DNA014 DNA007 LYS069 DNA012 DNA020 Isolates DNA018 DNA013 LYS093 LYS072 DNA021 DNA024 LYS037 LYS080 LYS027 LYS051 LYS083 Met01-3-F Met01-960-R 89% 100% 100% 50% 100% GCGCAGGATGTGGAAGTAG SATCGACATGCTSTGCTACC Met01-306-F Met01-1160-R sucA 100% 50% 100% 25% 100% YTCSGAGAGCATCGAGTTG GGMTCGRTCCACTTCATCA Met01-1035-F Met01-1758-R 89% 100% 100% 100% 100% GCCGTTGCAGTGGAAGAT GGGCAAGGACAAGGARATY Met02-352-F* Met02-1121-R* 100% 100% 100% 100% 100% AAGGACATCAAGGAGCAGGA ACSCGGTAKATGTCGAACAG rpoB Met02-2480-F Met02-3116-R 100% 100% 100% 100% 100% TGAAGGATGACGTGTTCACC TTCGACTCGTCGTACTGCTT * Combination of primers selected as marker for the rest of this study 81 82

14 83 Table S8 - Information for 98 Methylobacterium isolates successfully isolated, amplified and 84 sequenced for the rpoB marker from 2018 timeline (isolation batch 1/2). For this batch, 85 isolates were obtained from all samples collected from June to October 2018 (3-4 time replicates 86 per tree) on 4 trees in each forest (2 Acer saccharum (ASCA) and 2 Fagus grandifolia (FAGR)). 87 Isolation was performed at 20 and 30 °C on MMS media with methanol as sole carbon source.

Site Plot Tree Species Date 1 Date 2 Date 3 Date 4 MSH 27-Jun 6-Aug 7-Sep 18-Oct 1 1 FAGR 2 2 3 5 1 3 ACSA 7 1 1 1 3 1 ACSA 6 1 1 0 6 6 FAGR -* 4 1 1 Isolation yield per sample 5.0 2.0 1.5 1.8 SBL 20-Jun 16-Jul 16-Aug 20-Sep 1 2 FAGR 4 8 3 3 2 4 ACSA 0 4 1 2 3 7 ACSA 4 6 2 3 4 3 FAGR 2 5 6 9 Isolation yield per sample 2.5 5.8 3.0 4.3 * no sample available 88 89

15 90 Table S9 - Information for 69 Methylobacterium isolates successfully isolated, amplified and 91 sequenced for the rpoB marker from 2018 timeline (isolation batch 2/2). In batch 1, we 92 obtained maximum isolation yield per sample in date 1 for MSH (27 June, n=5.0 isolates/sample) 93 and in date 2 for SBL (16 July, n=5.8). For this batch, we thus selected these dates for this second 94 batch, focusing on host- associated diversity. In each forest, we selected 10 trees sampled at the 95 aforementioned dates and representative of diversity found on forests.

Site Plot Tree Species Isolates MSH data 1 (27-Jun) 1 2 FAGR 1 1 4 ACSA 5 1 5 FAGR 4 3 2 ACSA 3 3 3 ACSA 2 4 1 OSVI 2 4 2 ACSA 6 4 3 ACSA 3 4 4 OSVI 6 4 5 QURU 2 4 6 QURU 1 4 7 QURU 2 SBL date 2 (16-Jul) 1 3 ACRU 1 1 7 ACPE 1 1 10 ABBA 5 2 1 ACPE 0 2 2 ACRU 0 2 3 FAGR 2 2 6 ABBA 2 3 3 ABBA 3 3 8 ACRU 1 3 10 ACPE 6 4 4 ABBA 4 4 7 ACRU 7 96 97

16 98 Table S10 - Information on 187 isolates used for rpoB phylogeny, including 167 isolates 99 from timline survey (2018) and 20 isolates from pilot survey (2017). Clade assignation and 100 sample origin are indicated. Isolation batch refers to different batches of isolation: 2018 (from 101 MSH 2017 samples; here only isolates for which rpoB was sequenced are displayed; Tables 102 S6,S7); 2019-1 (from 2018 samples, first batch on 4 trees at four dates; Table S8); 2019-2 (from 103 2018 samples, second batch on 20 trees at one date; Table S9). Source sample name contains 104 following information: Forest-Plot-TreeID-Replicate. Symbol † indicates isolates used to build 105 the METH community.

Temp. of Tree Sampling Isolation Isolate Clade Source sample isolation species date batch (°C) DNA001 A1 MSH-H0-1-C ACSA 17-Aug-17 2018 20 DNA006 † A1 MSH-H0-1-A ACSA 17-Aug-17 2018 30 DNA007 † A6 MSH-L0-8-C FAGR 17-Aug-17 2018 20 DNA010 † A1 MSH-L0-1-C ACSA 17-Aug-17 2018 30 DNA011 A9 MSH-L0-1-C ACSA 17-Aug-17 2018 30 DNA012 † A9 MSH-L0-9-C FAGR 17-Aug-17 2018 20 DNA013 † A6 MSH-H0-10-B OSVI 17-Aug-17 2018 20 DNA014 A1 MSH-H0-2-C ACSA 17-Aug-17 2018 20 DNA018 † A1 MSH-H0-10-B OSVI 17-Aug-17 2018 20 DNA020 † A10 MSH-L0-8-C FAGR 17-Aug-17 2018 20 DNA021 † A10 MSH-H0-1-C ACSA 17-Aug-17 2018 30 DNA024 † A1 MSH-H0-6-B ACPE 17-Aug-17 2018 20 LYS027 A1 MSH-L0-7-C FAGR 17-Aug-17 2018 30 LYS037 A6 MSH-H0-10-B OSVI 17-Aug-17 2018 20 LYS051 A1 MSH-H0-10-B OSVI 17-Aug-17 2018 20 LYS069 A2 MSH-L0-2-C ACSA 17-Aug-17 2018 20 LYS072 A9 MSH-H0-9-C FAGR 17-Aug-17 2018 20 LYS080 A9 MSH-L0-1-A ACSA 17-Aug-17 2018 30 LYS083 A1 MSH-L0-2-C ACSA 17-Aug-17 2018 30 LYS093 A2 MSH-H0-5-A ACPE 17-Aug-17 2018 30 E-002 A9 MSH-06-06-F FAGR 07-Sep-18 2019-1 30 E-003 B MSH-01-03-F ACSA 07-Sep-18 2019-1 30 E-005 A9 MSH-01-01-F FAGR 07-Sep-18 2019-1 30 E-006 A9 SBL-03-07-B ACSA 20-Jun-18 2019-1 30 E-008 A9 MSH-03-01-B ACSA 27-Jun-18 2019-1 30 E-009 A9 MSH-03-01-B ACSA 27-Jun-18 2019-1 30 E-010 A9 SBL-02-04-D ACSA 16-Jul-18 2019-1 30 E-011 A9 SBL-03-07-D ACSA 16-Jul-18 2019-1 30 E-012 † A9 SBL-03-07-D ACSA 16-Jul-18 2019-1 30 E-016 A6 MSH-01-03-A ACSA 27-Jun-18 2019-1 20 E-020 A6 MSH-03-01-A ACSA 27-Jun-18 2019-1 20 E-021 † A9 SBL-04-03-A FAGR 20-Jun-18 2019-1 20 E-022 A9 MSH-01-03-A ACSA 27-Jun-18 2019-1 30 E-024 A9 MSH-06-06-C FAGR 06-Aug-18 2019-1 30 E-025 A6 MSH-01-03-C ACSA 06-Aug-18 2019-1 30 E-026 A9 SBL-01-02-B FAGR 20-Jun-18 2019-1 30 E-027 A9 SBL-01-02-B FAGR 20-Jun-18 2019-1 30 E-028 A9 SBL-04-03-D FAGR 16-Jul-18 2019-1 30 E-029 A9 SBL-01-02-D FAGR 16-Jul-18 2019-1 30 E-030 A6 SBL-01-02-D FAGR 16-Jul-18 2019-1 30 E-033 A9 SBL-04-03-H FAGR 20-Sep-18 2019-1 30 E-034 A9 SBL-04-03-H FAGR 20-Sep-18 2019-1 30 E-035 A9 SBL-01-02-H FAGR 20-Sep-18 2019-1 30

17 E-037 A6 SBL-01-02-C FAGR 16-Jul-18 2019-1 20 E-039 † A6 SBL-02-04-C ACSA 16-Jul-18 2019-1 20 E-040 A6 SBL-04-03-C FAGR 16-Jul-18 2019-1 20 E-041 A6 SBL-04-03-C FAGR 16-Jul-18 2019-1 20 E-042 A10 MSH-01-01-B FAGR 27-Jun-18 2019-1 20 E-045 A2 MSH-01-03-B ACSA 27-Jun-18 2019-1 20 E-046 A9 MSH-01-03-B ACSA 27-Jun-18 2019-1 20 E-047 A9 SBL-03-07-B ACSA 20-Jun-18 2019-1 20 E-048 B SBL-03-07-B ACSA 20-Jun-18 2019-1 20 E-061 A10 MSH-01-01-E FAGR 07-Sep-18 2019-1 30 E-062 A9 SBL-03-07-B ACSA 20-Jun-18 2019-1 20 E-063 A6 SBL-01-02-C FAGR 16-Jul-18 2019-1 20 E-064 B SBL-04-03-H FAGR 20-Sep-18 2019-1 30 E-065 A9 SBL-04-03-F FAGR 16-Aug-18 2019-1 30 E-066 A9 SBL-01-02-D FAGR 16-Jul-18 2019-1 30 J-001 A9 MSH-03-01-A ACSA 27-Jun-18 2019-1 30 J-002 A9 MSH-03-01-A ACSA 27-Jun-18 2019-1 30 J-003 A9 MSH-03-01-A ACSA 27-Jun-18 2019-1 30 J-005 A6 SBL-01-02-E FAGR 16-Aug-18 2019-1 20 J-008 A9 SBL-02-04-C ACSA 16-Jul-18 2019-1 30 J-009 A9 SBL-02-04-C ACSA 16-Jul-18 2019-1 30 J-010 A9 SBL-03-07-C ACSA 16-Jul-18 2019-1 30 J-011 A9 SBL-03-07-C ACSA 16-Jul-18 2019-1 30 J-014 B MSH-01-03-G ACSA 18-Oct-18 2019-1 30 J-015 A6 MSH-01-01-G FAGR 18-Oct-18 2019-1 20 J-017 A9 SBL-04-03-G FAGR 20-Sep-18 2019-1 30 J-018 A9 SBL-04-03-G FAGR 20-Sep-18 2019-1 30 J-019 A9 SBL-04-03-G FAGR 20-Sep-18 2019-1 30 J-021 A9 SBL-01-02-E FAGR 16-Aug-18 2019-1 30 J-022 A6 SBL-01-02-E FAGR 16-Aug-18 2019-1 30 J-026 † A9 SBL-04-03-F FAGR 16-Aug-18 2019-1 20 J-028 A9 SBL-03-07-E ACSA 16-Aug-18 2019-1 30 J-029 A6 SBL-04-03-E FAGR 16-Aug-18 2019-1 20 J-030 A9 SBL-04-03-E FAGR 16-Aug-18 2019-1 20 J-031 A6 SBL-02-04-G ACSA 20-Sep-18 2019-1 30 J-033 A9 SBL-03-07-G ACSA 20-Sep-18 2019-1 30 J-036 A9 SBL-02-04-F ACSA 16-Aug-18 2019-1 30 J-037 B SBL-01-02-G FAGR 20-Sep-18 2019-1 30 J-043 B MSH-01-01-H FAGR 18-Oct-18 2019-1 20 J-045 A9 SBL-03-07-F ACSA 16-Aug-18 2019-1 30 J-047 A2 MSH-03-01-F ACSA 07-Sep-18 2019-1 30 J-048 † A9 SBL-01-02-C FAGR 16-Jul-18 2019-1 30 J-049 A9 SBL-01-02-C FAGR 16-Jul-18 2019-1 30 J-050 A6 MSH-03-01-D ACSA 06-Aug-18 2019-1 20 J-051 A9 SBL-04-03-E FAGR 16-Aug-18 2019-1 30 J-052 A9 SBL-04-03-E FAGR 16-Aug-18 2019-1 30 J-054 A10 MSH-06-06-H FAGR 18-Oct-18 2019-1 30 J-056 † A1 MSH-01-01-D FAGR 06-Aug-18 2019-1 30 J-057 † A9 MSH-01-01-D FAGR 06-Aug-18 2019-1 30 J-059 A6 SBL-01-02-D FAGR 16-Jul-18 2019-1 20 J-062 † A6 MSH-01-01-F FAGR 07-Sep-18 2019-1 20 J-064 A9 SBL-03-07-D ACSA 16-Jul-18 2019-1 20 J-065 A6 SBL-04-03-H FAGR 20-Sep-18 2019-1 20 J-066 A9 MSH-06-06-D FAGR 06-Aug-18 2019-1 30 J-067 A10 MSH-06-06-D FAGR 06-Aug-18 2019-1 30 J-068 A1 MSH-06-06-D FAGR 06-Aug-18 2019-1 30 J-070 A9 SBL-04-03-A FAGR 20-Jun-18 2019-1 30 J-072 A9 SBL-04-03-C FAGR 16-Jul-18 2019-1 30 J-073 A6 SBL-04-03-C FAGR 16-Jul-18 2019-1 30 J-074 A9 SBL-03-07-H ACSA 20-Sep-18 2019-1 30 J-075 A9 SBL-03-07-H ACSA 20-Sep-18 2019-1 30 J-076 A10 MSH-01-01-H FAGR 18-Oct-18 2019-1 30

18 J-077 † A9 MSH-01-01-H FAGR 18-Oct-18 2019-1 30 J-078 A1 MSH-01-01-H FAGR 18-Oct-18 2019-1 30 J-082 A9 MSH-01-01-B FAGR 27-Jun-18 2019-1 30 J-083 A10 MSH-01-03-B ACSA 27-Jun-18 2019-1 30 J-084 † A1 MSH-01-03-B ACSA 27-Jun-18 2019-1 30 J-085 A9 MSH-01-03-B ACSA 27-Jun-18 2019-1 30 J-086 A9 SBL-04-03-G FAGR 20-Sep-18 2019-1 20 J-087 A9 SBL-04-03-G FAGR 20-Sep-18 2019-1 20 J-088 A9 SBL-02-04-G ACSA 20-Sep-18 2019-1 20 J-089 A6 SBL-01-02-B FAGR 20-Jun-18 2019-1 20 J-090 A1 SBL-01-02-B FAGR 20-Jun-18 2019-1 20 J-092 A6 SBL-03-07-C ACSA 16-Jul-18 2019-1 20 J-093 † A9 SBL-01-02-H FAGR 20-Sep-18 2019-1 30 E-101 A9 SBL-01-10-D ABBA 16-Jul-18 2019-2 30 E-102 A9 SBL-01-10-D ABBA 16-Jul-18 2019-2 30 E-103 A6 MSH-04-07-B QURU 27-Jun-18 2019-2 30 E-104 A9 MSH-04-02-B ACSA 27-Jun-18 2019-2 30 E-105 A6 MSH-04-02-B ACSA 27-Jun-18 2019-2 30 E-106 A6 MSH-04-02-B ACSA 27-Jun-18 2019-2 30 E-107 A9 MSH-04-04-B OSVI 27-Jun-18 2019-2 30 E-109 A9 MSH-04-03-B ACSA 27-Jun-18 2019-2 30 E-112 A6 MSH-01-02-B FAGR 27-Jun-18 2019-2 30 E-114 A9 SBL-01-07-D ACPE 16-Jul-18 2019-2 30 E-115 A9 SBL-04-07-D ACRU 16-Jul-18 2019-2 30 E-116 A9 SBL-04-07-D ACRU 16-Jul-18 2019-2 30 E-119 A9 MSH-03-03-B ACSA 27-Jun-18 2019-2 30 E-120 A6 MSH-01-04-B ACSA 27-Jun-18 2019-2 30 E-121 A9 MSH-01-04-B ACSA 27-Jun-18 2019-2 30 E-123 A5b SBL-01-03-D ACRU 16-Jul-18 2019-2 30 E-124 A9 SBL-04-04-D ABBA 16-Jul-18 2019-2 30 E-125 A9 SBL-04-04-D ABBA 16-Jul-18 2019-2 30 E-126 A9 SBL-03-03-D ABBA 16-Jul-18 2019-2 30 E-127 A9 SBL-03-03-D ABBA 16-Jul-18 2019-2 30 E-128 A9 SBL-03-03-D ABBA 16-Jul-18 2019-2 30 E-129 A9 SBL-03-10-D ACPE 16-Jul-18 2019-2 30 E-130 A9 SBL-03-10-D ACPE 16-Jul-18 2019-2 30 E-132 A1 MSH-03-02-B ACSA 27-Jun-18 2019-2 30 J-103 B MSH-04-06-A QURU 27-Jun-18 2019-2 30 J-104 A9 MSH-01-05-A FAGR 27-Jun-18 2019-2 30 J-105 A9 MSH-01-05-A FAGR 27-Jun-18 2019-2 30 J-106 A9 MSH-04-04-A OSVI 27-Jun-18 2019-2 30 J-107 A9 MSH-04-04-A OSVI 27-Jun-18 2019-2 30 J-108 A1 MSH-04-04-A OSVI 27-Jun-18 2019-2 30 J-111 A9 MSH-04-05-A QURU 27-Jun-18 2019-2 30 J-112 A2 MSH-04-05-A QURU 27-Jun-18 2019-2 30 J-113 A9 SBL-02-06-C ABBA 16-Jul-18 2019-2 30 J-115 A9 SBL-01-10-C ABBA 16-Jul-18 2019-2 30 J-116 A9 SBL-01-10-C ABBA 16-Jul-18 2019-2 30 J-117 A6 MSH-04-07-A QURU 27-Jun-18 2019-2 30 J-118 A9 SBL-04-07-C ACRU 16-Jul-18 2019-2 20 J-120 A9 SBL-03-10-C ACPE 16-Jul-18 2019-2 30 J-121 A9 SBL-03-10-C ACPE 16-Jul-18 2019-2 30 J-122 A9 SBL-03-10-C ACPE 16-Jul-18 2019-2 30 J-123 A9 SBL-04-04-C ABBA 16-Jul-18 2019-2 30 J-124 A9 SBL-04-04-C ABBA 16-Jul-18 2019-2 30 J-125 A6 MSH-01-04-A ACSA 27-Jun-18 2019-2 30 J-127 A9 SBL-02-03-C FAGR 16-Jul-18 2019-2 30 J-128 A9 SBL-02-03-C FAGR 16-Jul-18 2019-2 30 J-130 A6 SBL-04-07-C ACRU 16-Jul-18 2019-2 30 J-131 A6 SBL-04-07-C ACRU 16-Jul-18 2019-2 20 J-132 A9 MSH-04-02-B ACSA 27-Jun-18 2019-2 20 J-133 A9 MSH-04-02-B ACSA 27-Jun-18 2019-2 20

19 J-134 A6 MSH-04-02-B ACSA 27-Jun-18 2019-2 20 J-135 A9 MSH-04-03-B ACSA 27-Jun-18 2019-2 20 J-136 A6 MSH-04-04-A OSVI 27-Jun-18 2019-2 20 J-137 A6 MSH-04-03-A ACSA 27-Jun-18 2019-2 20 J-138 A9 MSH-04-01-A OSVI 27-Jun-18 2019-2 20 J-139 A6 MSH-04-01-A OSVI 27-Jun-18 2019-2 20 J-141 A9 MSH-01-04-A ACSA 27-Jun-18 2019-2 20 J-142 A6 SBL-03-10-D ACPE 16-Jul-18 2019-2 20 J-146 A6 MSH-03-02-A ACSA 27-Jun-18 2019-2 20 J-147 A9 SBL-04-07-D ACRU 16-Jul-18 2019-2 20 J-148 A9 SBL-04-07-D ACRU 16-Jul-18 2019-2 20 J-150 A6 SBL-02-06-C ABBA 16-Jul-18 2019-2 20 J-152 A6 MSH-04-04-B OSVI 27-Jun-18 2019-2 20 J-153 A1 MSH-03-03-A ACSA 27-Jun-18 2019-2 20 J-156 A6 MSH-03-02-B ACSA 27-Jun-18 2019-2 20 J-158 A9 SBL-01-10-C ABBA 16-Jul-18 2019-2 20 J-160 A6 MSH-01-05-B FAGR 27-Jun-18 2019-2 20 J-162 A1 MSH-01-05-B FAGR 27-Jun-18 2019-2 20 J-163 A6 MSH-01-04-B ACSA 27-Jun-18 2019-2 20 J-164 A9 SBL-03-08-C ACRU 16-Jul-18 2019-2 20 106 107

20 108 Table S11 - Summary of ASV taxonomic annotation before correction by rpoB phylogeny - 109 ASV number (ASV) and relative abundance (F; proportion of sequences) in METH community 110 (n=4) and in phyllosphere samples (n=184). Raw taxonomic assignation from a rpoB nucleotide 111 database modified from Ogier et al. (76) and limited to Alphaproteobacteria. For each taxon, the 112 following information is shown: the number of ASVs and the average relative abundance of their 113 sequences (F), both in METH community (positive control; n=4) and phyllosphere samples 114 (n=184).

Meth Samples Class Order Family Genus Clade ASV F ASV F Alphaproteobacteria 45 100% 1399 100% unknown 1 0.02% 31 0.29% Rhodobacterales 0 - 1 0.00%

Rickettsiales 0 - 5 0.02%

Rhodospirillales 0 - 10 0.23%

Sphingomonadales 1 0.49% 22 0.22%

Caulobacterales 0 - 198 4.32%

Rhizobiales 43 99.49% 1132 94.91% unknown 2 0.02% 360 21.20%

Brucellaceae 0 - 1 0.03%

Rhizobiaceae 0 - 6 0.10%

Aurantimonadaceae 0 - 13 0.21%

Phyllobacteriaceae 0 - 19 0.20%

Hyphomicrobiaceae 0 - 22 0.31%

Bradyrhizobiaceae 0 - 78 0.78%

Methylocystaceae 0 - 9 0.10% Beijerinckiaceae 6 0.13% 131 22.53%

Lichenibacteriaceae 13 0.17% 262 25.68%

Methylobacteriaceae 22 99.18% 231 23.78%

unknown 0 - 20 0.51% Enterovirga 0 - 6 0.18%

Microvirga 0 - 4 0.03%

Methylobacterium 22 99.18% 201 23.06% A1 6 24.66% 32 2.58%

A2 0 - 5 0.04%

A4 1 0.01% 12 0.22%

A5 0 - 13 0.29%

A6 4 9.34% 31 6.56%

A9 8 57.41% 56 9.52%

A10 2 7.74% 2 0.16%

B 0 - 9 0.80%

unknown 1 0.02% 41 2.88% 115 116 117

21 118 Table S12 - Summary of ASV taxonomic annotation after correction by rpoB phylogeny - 119 ASV number (ASV) and relative abundance (F ; proportion of sequences) in METH community 120 (n=4) and in phyllosphere samples (n=184) after taxonomy correction by phylogeny). For each 121 taxon, the following information is shown: the number of ASVs and the average relative 122 abundance of their sequences (F), both in Meth community (positive control; n=4) and 123 phyllosphere samples (n=184).

Meth Samples Class Order Family Genus ASV F ASV F Alphaproteobacteria 45 100% 1399 100% unknown 1 0.02% 19 0.15% Rhodobacterales 0 - 1 0.00%

Rickettsiales 0 - 5 0.02%

Rhodospirillales 0 - 10 0.23%

Sphingomonadales 1 0.49% 22 0.22%

Caulobacterales 0 - 209 4.42%

Rhizobiales 43 99.49% 1133 94.96% unknown 0 - 56 1.18%

Brucellaceae 0 - 1 0.03%

Rhizobiaceae 0 - 6 0.10%

Aurantimonadaceae 0 - 22 0.33%

Phyllobacteriaceae 0 - 19 0.20%

Hyphomicrobiaceae 0 - 23 0.33%

Bradyrhizobiaceae 0 - 80 0.79%

Methylocystaceae-like 2 0.02% 171 11.04%

Beijerinckiaceae (GroupRH) 6 0.13% 165 24.58%

Lichenibacteriaceae 13 0.17% 307 31.75%

Methylobacteriaceae 22 99.18% 283 24.65%

Enterovirga 0 - 78 1.56% Microvirga 0 - 5 0.04%

Methylobacterium 22 99.18% 200 23.05% 124 125

22 126 Table S13 - Methylobacterium ASV diversity and comparison with estimation from isolation 127 (2018). The following information is shown: clade assignation based on monophyly with 128 reference genomes and isolates (unassigned marked as “un”), number of ASVs per clade, number 129 of isolates per clades, ASV relative abundance (proportion of Methylobacterium ASV sequences 130 assigned to this clade), number of ASVs and corresponding isolates having 100% or 98.5% 131 nucleotide sequence identity and corresponding relative abundance for these ASVs (F).

ASV abundance (F) 100% sequence match 98.5% sequence match Clade ASVs Isolates All MSH SBL ASVs Isolates F ASVs Isolates F A1 31 9 0.066 0.133 0.008 4 4 0.022 26 7 0.063 A2 7 3 0.003 0.003 0.003 1 1 0.001 4 1 0.002 A3 2 - 0.001 0.001 0.002 ------A4 20 - 0.017 0.026 0.010 ------A5 3 1 0.001 0.001 - 1 1 0.001 1 1 0.001 A6 37 41 0.243 0.326 0.172 16 28 0.192 27 40 0.232 A9 59 100 0.452 0.388 0.508 27 83 0.387 54 95 0.434 A10 6 6 0.010 0.012 0.009 2 3 0.006 2 4 0.006 B 31 7 0.191 0.102 0.268 2 3 0.105 10 7 0.122 un 4 - 0.015 0.008 0.021 ------Total 200 167 1 1 1 53 123 0.712 124 155 0.859 Part of total diversity 26.5% 73.7% 71.2% 62.0% 92.8% 85.9% 132 133

23 134 Table S14 - PERMANOVA analysis of 184 phyllosphere Methylobacterium samples assessed 135 by rpoB barcoding (200 ASVs). Part of variance in community composition (ASV relative 136 abundance, Hellinger transformation, Bray-Curtis dissimilarity) explained by each factor and 137 their interactions (“***”: p<0.00l; “**”: p<0.01; “*”: p<0.05). All samples MSH SBL Samples 184 85 99 Forest (F) 0.311*** - - Host tree species (H) 0.074*** 0.121*** 0.119*** Sampling date (D) 0.048*** 0.121*** 0.043** Plot (P) 0.079*** 0.084*** 0.122*** F:H 0.004 - - H:D 0.073* 0.108* 0.104 H:P 0.045** 0.023 0.087* D:P 0.058 0.117 0.068 H:D:P 0.083 0.037 0.164 Residuals 0.225 0.389 0.294 138 139

24 140 Table S15 - Summary of statistics from autocorrelation analyzes on 184 phyllosphere 141 Methylobacterium samples assessed by rpoB barcoding (200 ASVs). For each model, pairwise 142 dissimilarity between two communities was assessed with the Bray-Curtis dissimilarity index 143 (BC) from ASV relative abundance (Hellinger transformation) under a linear model. Spatial 144 autocorrelation general models : BC in function of pairwise spatial distance separating two 145 sampled trees (pDist) and date of sampling (Date) and their interaction (pDist:Date). Samples 146 from forests MSH and SBL were analyzed separately (two models). Only pairwise comparisons 147 among samples from a same date were considered. Spatial autocorrelation models per date: BC 148 in function of pairwise spatial distance (pDist). Each sampling date (n=4) and forest (n=2) was 149 analyzed separately (eight models). Temporal autocorrelation: general models: BC in function of 150 pairwise spatial time separating two sampled trees (pTime). Samples from forests MSH and SBL 151 were analyzed separately (two models) and all spatial scales were considered. For each model, 152 the average and standard deviation of the intercept (mean BC value) are indicated. For each 153 factor (pDist, Date, pDist:Date and pTime), the average and standard deviation of estimates 154 (slope) are indicated. Significance of estimates was assessed by ANOVA (“***”: p<0.00l; “**”: 155 p<0.01; “*”: p<0.05).

Categories (n) Intercept (sd) Estimates*10-3 (sd) Spatial autocorrelation general models: lm(BC∼pDist*D) Site (within dates) BC pDist D pDist:Date MSH 0.5965 (0.0107) -0.0041 (0.0192)*** -2.7648 (0.1313)*** 0.0007 (0.0002)** SBL 0.6493 (0.0097) 0.0157 (0.0145) -1.5575 (0.1646)*** 0.0000 (0.0002) Spatial autocorrelation models per date: lm(BC∼pDist) Site Date BC pDist MSH 27 Jun. 0.6237 (0.0340) -0.0425 (0.0725) 6 Aug. 0.4919 (0.0112) 0.0503 (0.0192)** 7 Sept. 0.3746 (0.0059) 0.0313 (0.0099)** 18 Oct. 0.2966 (0.0045) 0.0795 (0.0073)*** SBL 20 Jun. 0.6868 (0.0146) 0.0082 (0.0216) 16 Jul. 0.5819 (0.0113) 0.0215 (0.0174) 16 Aug. 0.5415 (0.0105) 0.0114 (0.0150) 20 Sept. 0.5222 (0.0089) 0.0145 (0.0130) Temporal autocorrelation general models (BC∼pTime) Site BC pTime MSH 0.4086 (0.0032) 1.0786 (0.0607)*** SBL 0.5789 (0.0030) 0.3012 (0.0617)*** 156

25 157 Table S16 - List of 79 Methylobacterium isolates monitored for growth performance under 158 four temperature treatments (see Table S10 for information on isolates). Average yield and 159 rate values were estimated from 1-5 replicates for each Methylobacterium isolate (n=79) and 160 temperature treatment (n=4). NA values indicate that no growth could be detected during the 161 monitoring step for a given isolate under a given temperature treatment. YIELD RATE Isolates P20M20 P20M30 P30M20 P30M30 P20M20 P20M30 P30M20 P30M30 E-002 5.67 6.06 6.87 4.34 0.089 0.051 0.067 0.062 E-003 23.87 14.72 21.06 14.42 0.076 0.105 0.074 0.068 E-005 2.86 2.88 2.22 2.44 0.090 0.119 0.090 0.111 E-006 10.34 9.28 6.34 4.56 0.067 0.062 0.057 0.054 E-009 0.75 1.31 0.73 1.23 0.071 0.089 0.090 0.102 E-010 13.53 2.19 15.31 5.62 0.105 0.100 0.077 0.075 E-011 6.77 6.88 9.54 5.23 0.067 0.091 0.073 0.112 E-012 6.15 3.44 3.04 1.83 0.059 0.097 0.054 0.089 E-016 6.51 5.96 5.32 8.35 0.053 0.056 0.057 0.045 E-020 4.86 4.55 4.70 5.55 0.048 0.074 0.045 0.052 E-021 5.70 2.44 6.98 3.41 0.071 0.085 0.093 0.116 E-022 9.65 4.52 7.75 4.62 0.054 0.144 0.051 0.147 E-025 0.89 2.47 0.84 1.57 0.088 0.126 0.119 0.086 E-026 6.32 5.21 6.98 4.74 0.088 0.092 0.060 0.105 E-027 8.38 4.53 6.59 3.98 0.064 0.086 0.062 0.080 E-028 12.52 5.88 12.96 7.05 0.071 0.079 0.072 0.064 E-030 4.92 7.82 4.93 6.52 0.070 0.078 0.051 0.063 E-035 11.15 5.82 13.66 8.22 0.087 0.110 0.072 0.096 E-039 2.85 2.90 2.32 1.65 0.075 0.076 0.068 0.101 E-040 1.80 1.82 2.92 1.71 0.065 0.072 0.069 0.127 E-041 1.33 3.26 1.01 2.27 0.063 0.091 0.061 0.118 E-042 4.10 3.43 2.11 2.29 0.073 0.140 0.114 0.130 E-045 19.70 6.85 8.92 9.26 0.109 0.148 0.063 0.101 E-046 7.87 11.47 19.40 7.65 0.055 0.072 0.102 0.163 E-047 15.73 8.01 11.02 8.06 0.055 0.068 0.059 0.089 E-061-B 13.47 8.50 13.04 8.16 0.079 0.116 0.073 0.138 E-061-R 11.79 8.72 10.27 6.06 0.073 0.089 0.076 0.098 E-062 10.92 9.17 13.46 11.39 0.101 0.075 0.072 0.088 E-063 0.13 0.85 0.75 1.09 0.077 0.067 0.085 0.081 E-064 12.00 6.19 8.24 5.03 0.092 0.161 0.094 0.162 E-065 3.67 2.71 3.41 2.32 0.033 0.114 0.065 0.143 E-066 21.99 13.15 15.13 11.30 0.088 0.092 0.079 0.091 J-002 8.76 4.59 9.66 4.57 0.060 0.057 0.063 0.063 J-005 1.30 2.82 1.19 1.55 0.064 0.093 0.098 0.084 J-008 5.43 4.31 9.22 5.60 0.059 0.096 0.066 0.073 J-009 6.75 4.19 8.35 3.66 0.043 0.053 0.068 0.066 J-010 15.32 7.73 16.28 7.40 0.066 0.136 0.075 0.127 J-014 14.65 11.74 16.77 13.36 0.134 0.124 0.112 0.139 J-015 6.97 3.79 7.90 4.93 0.064 0.110 0.072 0.129 J-019 8.54 3.00 11.30 9.16 0.079 0.114 0.073 0.133 J-022 2.03 1.62 5.85 1.81 0.085 0.093 0.082 0.080 J-026 3.10 3.07 1.95 3.10 0.099 0.145 0.149 0.132 J-029 1.31 3.02 2.76 0.94 0.100 0.105 0.069 0.138 J-030 2.47 2.73 0.50 0.24 0.074 0.041 0.076 0.065 J-031 0.85 0.88 0.34 0.21 0.077 0.092 0.077 0.105

26 J-036 12.03 10.06 8.72 7.59 0.044 0.118 0.041 0.091 J-037 14.08 11.15 13.34 11.74 0.112 0.119 0.120 0.121 J-043 13.46 4.81 9.34 4.86 0.118 0.158 0.121 0.128 J-045 3.37 4.92 2.40 3.54 0.103 0.117 0.062 0.117 J-047 10.69 5.10 9.72 5.00 0.130 0.113 0.137 0.163 J-048 9.32 5.91 7.80 4.46 0.077 0.114 0.070 0.088 J-050 0.83 0.72 0.70 0.96 0.083 0.105 0.070 0.065 J-052 NA NA NA 0.10 NA NA NA 0.076 J-054 NA 7.47 1.24 0.70 NA 0.100 0.081 0.074 J-056 1.61 1.48 0.82 0.88 0.104 0.103 0.091 0.087 J-057 3.93 2.76 0.86 0.72 0.085 0.136 0.057 0.060 J-059 5.74 2.16 1.81 1.48 0.050 0.081 0.074 0.084 J-062 1.25 1.65 0.77 1.04 0.109 0.083 0.084 0.121 J-064 4.10 4.76 4.05 5.61 0.059 0.126 0.064 0.132 J-065 2.86 2.57 0.98 1.28 0.084 0.089 0.072 0.077 J-067 18.82 5.61 1.71 1.00 0.054 0.059 0.065 0.104 J-068 2.44 0.93 2.67 0.59 0.141 0.067 0.162 0.163 J-070 10.90 12.96 10.07 13.45 0.051 0.051 0.058 0.071 J-072 18.69 10.69 17.43 9.43 0.053 0.063 0.054 0.080 J-073 2.13 2.92 3.23 3.07 0.080 0.097 0.075 0.113 J-074 12.20 16.95 13.35 14.53 0.048 0.058 0.042 0.055 J-076 3.64 6.64 3.67 2.63 0.075 0.102 0.079 0.100 J-077 7.77 8.06 10.88 8.44 0.070 0.120 0.078 0.135 J-078 6.28 6.14 4.82 6.10 0.070 0.107 0.069 0.120 J-082 1.60 1.84 1.86 1.54 0.108 0.130 0.060 0.101 J-083 4.07 3.12 3.88 2.04 0.049 0.089 0.058 0.087 J-084 0.43 0.83 0.18 0.17 0.077 0.091 0.077 0.159 J-085 8.83 6.46 9.92 6.01 0.069 0.061 0.060 0.096 J-086 7.23 3.27 6.87 2.82 0.072 0.116 0.074 0.131 J-087 7.73 2.88 7.02 2.18 0.082 0.104 0.065 0.161 J-088 3.68 2.20 3.25 1.15 0.084 0.147 0.078 0.156 J-090 4.42 0.49 0.70 0.86 0.093 0.064 0.103 0.072 J-092 2.47 1.50 1.79 1.52 0.066 0.108 0.064 0.096 J-093 8.92 7.62 4.74 4.02 0.084 0.071 0.073 0.134 162

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