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The following supplement accompanies the article

Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake

Mylène Hugoni, Agnès Vellet, Didier Debroas*

*Corresponding author: [email protected]

Aquatic Microbial Ecology 79:115–125 (2017)

Table S1. Phylogenetic affiliation of the surface micro-layer (SML) specific OTUs, the epilimnion (E) specific OTUs and shared to both layers. OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared ;Acidobacteria;Acidobacteriales;Acidobacteriaceae (Subgroup 1);Granulicella; 2 0 0 Acidobacteria;Acidobacteria;Acidobacteriales;Acidobacteriaceae (Subgroup 1);uncultured; 1 0 0 Acidobacteria;Acidobacteria;JG37-AG-116; 24 0 0 Acidobacteria;Acidobacteria;Subgroup 13; 0 1 0 Acidobacteria;Acidobacteria;Subgroup 3;Family ;Bryobacter; 0 0 1 Acidobacteria;Acidobacteria;Subgroup 3;SJA-149; 0 1 1 Acidobacteria;Acidobacteria;Subgroup 4;RB41; 0 1 0 Acidobacteria;Acidobacteria;Subgroup 6; 0 0 1 ;AcI;AcI-A; 0 4 13 Actinobacteria;AcI;AcI-A;AcI-A3; 0 4 0 Actinobacteria;AcI;AcI-A;AcI-A5; 3 1 1 Actinobacteria;AcI;AcI-A;AcI-A7; 0 1 0 Actinobacteria;AcI;AcI-B;AcI-B1; 0 8 1 Actinobacteria;AcI;AcI-B;AcI-B2; 0 7 0 Actinobacteria;Acidimicrobia;Acidimicrobiales;;CL500-29 marine group; 7 34 11 Actinobacteria;Acidimicrobia;Acidimicrobiales;Family Incertae Sedis;Candidatus Microthrix; 0 1 0 Actinobacteria;Acidimicrobia;Acidimicrobiales;uncultured; 0 4 1 Actinobacteria;AcIV; 0 2 0 Actinobacteria;AcIV;Iluma-A2; 0 10 0

1 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Actinobacteria;AcIV;Iluma-B2; 0 1 0 Actinobacteria;AcTH1-A1; 0 4 2 Actinobacteria;Actinobacteria;Corynebacteriales;Corynebacteriaceae;; 2 0 0 Actinobacteria;Actinobacteria;Corynebacteriales;;; 0 0 1 Actinobacteria;Actinobacteria;Corynebacteriales;;Gordonia; 0 1 0 Actinobacteria;Actinobacteria;Corynebacteriales;Nocardiaceae;; 1 4 0 Actinobacteria;Actinobacteria;Corynebacteriales;Nocardiaceae;; 0 2 2 Actinobacteria;Actinobacteria;Corynebacteriales;Nocardiaceae;Williamsia; 0 1 0 Actinobacteria;Actinobacteria;Frankiales;Frankiaceae;; 2 0 0 Actinobacteria;Actinobacteria;Frankiales;; 0 9 3 Actinobacteria;Actinobacteria;Frankiales;Sporichthyaceae;Candidatus Planktophila; 0 5 3 Actinobacteria;Actinobacteria;Frankiales;Sporichthyaceae;hgcI ; 3 44 23 Actinobacteria;Actinobacteria;;;Brachybacterium; 1 0 0 Actinobacteria;Actinobacteria;Micrococcales;;Alpinimonas; 0 0 3 Actinobacteria;Actinobacteria;Micrococcales;Microbacteriaceae;Candidatus Limnoluna; 0 1 0 Actinobacteria;Actinobacteria;Micrococcales;Microbacteriaceae;Candidatus Planktoluna; 0 2 1 Actinobacteria;Actinobacteria;Micrococcales;Microbacteriaceae;; 0 1 0 Actinobacteria;Actinobacteria;Micrococcales;Microbacteriaceae;ML602J-51; 0 1 0 Actinobacteria;Actinobacteria;Micrococcales;Microbacteriaceae;MWH-Ta3; 0 1 1 Actinobacteria;Actinobacteria;Micrococcales;;; 0 3 0 Actinobacteria;Actinobacteria;PeM15; 0 1 0 Actinobacteria;Actinobacteria;;;; 0 1 0 Actinobacteria;Actinobacteria;Propionibacteriales;Propionibacteriaceae;; 16 0 0 Actinobacteria;Actinobacteria;Pseudonocardiales;;Pseudonocardia; 0 2 0 Actinobacteria;;Gaiellales;uncultured; 11 1 0 Actinobacteria;Thermoleophilia;;Patulibacteraceae;; 0 1 0 ;Armatimonadia;Armatimonadales; 3 1 5 Armatimonadetes;Armatimonadia;Armatimonadales;Armatimonadaceae;Armatimonas; 0 2 0 Armatimonadetes;unclassified Armatimonadetes; 0 0 2 ;Algor; 0 1 0 Bacteroidetes;Aquir; 0 8 0 Bacteroidetes;Bacteroidia;;Marinilabiaceae;uncultured; 0 2 0 Bacteroidetes;Bacteroidia;Bacteroidales;;vadinBC27 wastewater-sludge group; 0 1 0 Bacteroidetes;Cytophagia;;;uncultured; 0 3 4 Bacteroidetes;Cytophagia;Cytophagales;;; 3 1 4 Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae;; 0 2 0 Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae;; 1 2 1

2 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae;Hymenobacter; 2 0 0 Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae;; 0 1 0 Bacteroidetes;Cytophagia;Cytophagales;Cytophagaceae;Siphonobacter; 0 1 0 Bacteroidetes;Cytophagia;Cytophagales;;; 0 1 2 Bacteroidetes;Cytophagia;Cytophagales;MWH-CFBk5; 0 1 0 Bacteroidetes;Flavo; 0 1 1 Bacteroidetes;Flavobacteria;;Blattabacteriaceae;Candidatus Sulcia; 0 10 0 Bacteroidetes;Flavobacteria;Flavobacteriales;;Fluviicola; 0 11 5 Bacteroidetes;Flavobacteria;Flavobacteriales;Cryomorphaceae;uncultured; 0 2 1 Bacteroidetes;Flavobacteria;Flavobacteriales;;; 2 0 0 Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;; 5 31 14 Bacteroidetes;Flavobacteria;Flavobacteriales;NS9 marine group; 0 7 2 Bacteroidetes;FukuN47; 0 3 2 Bacteroidetes;PRD18D09; 1 1 10 Bacteroidetes;;;;; 0 4 0 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Chitinophagaceae;; 0 1 0 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Chitinophagaceae;Hydrotalea; 1 5 5 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Chitinophagaceae;; 0 15 12 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Chitinophagaceae;uncultured; 2 2 5 Bacteroidetes;Sphingobacteria;Sphingobacteriales;env.OPS 17; 4 5 4 Bacteroidetes;Sphingobacteria;Sphingobacteriales;LiUU-11-161; 0 7 3 Bacteroidetes;Sphingobacteria;Sphingobacteriales;NS11-12 marine group; 13 16 1 Bacteroidetes;Sphingobacteria;Sphingobacteriales;;Saprospira; 0 2 0 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Saprospiraceae;uncultured; 0 1 0 Bacteroidetes;Sphingobacteria;Sphingobacteriales;;; 1 0 0 Bacteroidetes;Sphingobacteria;Sphingobacteriales;Sphingobacteriaceae;; 0 2 0 Bacteroidetes;vadinHA17; 1 1 0 BD1-5;unclassified BD1-5; 0 1 0 Caldiserica;Caldisericia;Caldisericales;Caldisericaceae;; 0 1 0 Candidate division OD1;unclassified Candidate division OD1; 2 6 0 Candidate division OP11;unclassified Candidate division OP11; 1 2 0 Candidate division TM7;unclassified Candidate division TM7; 0 2 1 ;Chlamydiae;;;Candidatus ; 0 1 0 Chlorobi;Chlorobia;Chlorobiales;OPB56; 0 3 0 Chlorobi;Ignavibacteria;Ignavibacteriales;PHOS-HE36; 1 1 0 Chlorobi;Ignavibacteria;Ignavibacteriales;SR-FBR-L83; 0 1 0 ;Anaerolineae;Anaerolineales;Anaerolineaceae;uncultured; 0 1 0

3 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Chloroflexi;Caldilineae;Caldilineales;Caldilineaceae;uncultured; 0 2 0 Chloroflexi;Chloroflexia;Chloroflexales;Roseiflexaceae;Roseiflexus; 0 6 0 Chloroflexi;Dehalococcoidia;GIF9; 1 4 0 Chloroflexi;P2-11E; 0 1 0 ;; 12 48 16 Cyanobacteria;Cyanobacteria;SubsectionI;FamilyI;uncultured; 0 4 0 Cyanobacteria;Cyanobacteria;SubsectionIII;FamilyI;Limnothrix; 0 3 0 Cyanobacteria;Cyanobacteria;SubsectionIII;FamilyI;uncultured; 1 0 0 Cyanobacteria;Cyanobacteria;SubsectionIV;FamilyI; 48 0 16 -Thermus;Deinococci;Deinococcales;Trueperaceae;Truepera; 0 1 0 ;Fibrobacteria;Fibrobacterales;Fibrobacteraceae;uncultured; 0 1 0 ;;;;Bacillus; 0 1 0 Firmicutes;Bacilli;Bacillales;Paenibacillaceae; 0 1 0 Firmicutes;Bacilli;Bacillales;;Staphylococcus; 5 0 0 Firmicutes;Bacilli;Lactobacillales;;; 0 1 0 Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;; 1 0 0 Firmicutes;;Clostridiales;Caldicoprobacteraceae;Caldicoprobacter; 1 0 0 Firmicutes;Clostridia;Clostridiales;Family XI Incertae Sedis;; 1 0 0 Firmicutes;Clostridia;Clostridiales;Family XII Incertae Sedis;Fusibacter; 1 0 0 Firmicutes;Clostridia;Clostridiales;Family XIV Incertae Sedis;Anaerobranca; 0 1 0 Firmicutes;Clostridia;Clostridiales;Family XVII Incertae Sedis;uncultured; 3 0 0 Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Incertae Sedis; 21 0 0 Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;uncultured; 1 0 0 Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;Incertae Sedis; 11 1 0 Firmicutes;Clostridia;Clostridiales;Ruminococcaceae;uncultured; 3 2 0 Firmicutes;Clostridia;Clostridiales;Syntrophomonadaceae;uncultured; 4 0 0 Firmicutes;Clostridia;;;; 1 0 0 Firmicutes;;;Veillonellaceae;Selenomonas; 2 1 1 Firmicutes;OPB54; 2 0 0 ;Gemmatimonadetes;Gemmatimonadales;Gemmatimonadaceae;Gemmatimonas; 0 2 0 ;Lentisphaeria; 0 1 0 Lentisphaerae;Lentisphaeria;WCHB1-41; 0 3 0 ;Phycisphaerae;Phycisphaerales;Phycisphaeraceae;AKYG587; 0 1 0 Planctomycetes;Phycisphaerae;Phycisphaerales;Phycisphaeraceae;FS140-16B-02 marine group; 0 8 0 Planctomycetes;Phycisphaerae;Phycisphaerales;Phycisphaeraceae;SM1A02; 2 0 1 Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;Pirellula; 0 6 0 Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;Planctomyces; 1 3 0

4 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;Schlesneria; 0 3 0 Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;uncultured; 4 6 0 Planctomycetes;Planctomycetacia;Planctomycetales;Planctomycetaceae;Zavarzinella; 9 0 1 Planctomycetes;vadinHA49; 1 1 0 ;;A0904; 1 0 2 Proteobacteria;Alphaproteobacteria;AlphaII; 0 1 0 Proteobacteria;Alphaproteobacteria;;;Brevundimonas; 0 14 0 Proteobacteria;Alphaproteobacteria;Caulobacterales;Caulobacteraceae;Caulobacter; 6 9 7 Proteobacteria;Alphaproteobacteria;Caulobacterales;Caulobacteraceae;Phenylobacterium; 0 1 0 Proteobacteria;Alphaproteobacteria;Caulobacterales;Caulobacteraceae;uncultured; 0 3 0 Proteobacteria;Alphaproteobacteria;Caulobacterales;;Hirschia; 0 1 0 Proteobacteria;Alphaproteobacteria;LD12; 0 6 2 Proteobacteria;Alphaproteobacteria;Rhizobiales;1174-901-12; 1 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;alphaI cluster; 1 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Beijerinckiaceae;Methylovirgula; 1 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Bradyrhizobiaceae;Bosea; 0 3 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Bradyrhizobiaceae;Bradyrhizobium; 0 3 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Bradyrhizobiaceae;Rhodopseudomonas; 0 4 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Brucellaceae;Ochrobactrum; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;FukuN57; 1 6 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Hyphomicrobiaceae;Devosia; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Hyphomicrobiaceae;; 4 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Hyphomicrobiaceae;; 14 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;MNG7; 1 1 1 Proteobacteria;Alphaproteobacteria;Rhizobiales;Phyllobacteriaceae;Nitratireductor; 14 0 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Phyllobacteriaceae;Pseudaminobacter; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Phyllobacteriaceae;uncultured; 0 2 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Kaistia; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium; 1 0 0 Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Gemmobacter; 0 7 1 Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Leisingera; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Paracoccus; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Rhodobacter; 1 7 1 Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;uncultured; 0 1 0 Proteobacteria;Alphaproteobacteria;; 0 1 1 Proteobacteria;Alphaproteobacteria;Rhodospirillales;;; 1 0 0 Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acidocella; 51 3 0

5 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Roseococcus; 0 4 0 Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Roseomonas; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;uncultured; 7 1 0 Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Zavarzinia; 0 1 0 Proteobacteria;Alphaproteobacteria;Rhodospirillales;Rhodospirillaceae;Azospirillum; 12 0 0 Proteobacteria;Alphaproteobacteria;; 15 1 0 Proteobacteria;Alphaproteobacteria;Rickettsiales;Family Incertae Sedis;Candidatus Captivus; 0 4 0 Proteobacteria;Alphaproteobacteria;Rickettsiales;Family Incertae Sedis;Candidatus Hepatincola; 2 2 1 Proteobacteria;Alphaproteobacteria;Rickettsiales;Holosporaceae;uncultured; 0 1 0 Proteobacteria;Alphaproteobacteria;Rickettsiales;LWSR-14; 0 5 0 Proteobacteria;Alphaproteobacteria;Rickettsiales;mitochondria; 0 2 0 Proteobacteria;Alphaproteobacteria;Rickettsiales;Rickettsiaceae;Rickettsia; 0 1 0 Proteobacteria;Alphaproteobacteria;SAR11 clade;LD12 freshwater group; 0 4 7 Proteobacteria;Alphaproteobacteria;Sphingomonadales; 1 1 0 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Erythrobacteraceae;Porphyrobacter; 0 1 0 Proteobacteria;Alphaproteobacteria;Sphingomonadales;GOBB3-C201; 21 6 9 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Novosphingobium; 0 2 0 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sandarakinorhabdus; 0 1 3 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingobium; 1 1 0 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingomonas; 4 2 4 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingopyxis; 0 2 0 Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Zymomonas; 0 1 0 Proteobacteria;;BetIII; 3 2 4 Proteobacteria;Betaproteobacteria;;;Bordetella; 1 0 0 Proteobacteria;Betaproteobacteria;Burkholderiales;Alcaligenaceae;Derxia; 5 0 0 Proteobacteria;Betaproteobacteria;Burkholderiales;BetaI; 3 3 6 Proteobacteria;Betaproteobacteria;Burkholderiales;BetaI;Lhab; 0 3 3 Proteobacteria;Betaproteobacteria;Burkholderiales;BetaII;Polynucleobacter; 9 6 10 Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Burkholderia; 4 0 0 Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Limnobacter; 2 0 0 Proteobacteria;Betaproteobacteria;Burkholderiales;Burkholderiaceae;Ralstonia; 0 1 0 Proteobacteria;Betaproteobacteria;Burkholderiales;;Acidovorax; 10 2 5 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Albidiferax; 4 1 7 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Chlorochromatium; 1 18 3 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Comamonas; 0 0 1 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Limnohabitans; 1 0 0 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Paucibacter; 4 0 0

6 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Polaromonas; 0 0 4 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Rhizobacter; 5 2 5 Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;uncultured; 5 2 1 Proteobacteria;Betaproteobacteria;Burkholderiales;LbIV (ou betVII); 0 1 0 Proteobacteria;Betaproteobacteria;Burkholderiales;;Herbaspirillum; 3 4 3 Proteobacteria;Betaproteobacteria;Burkholderiales;Oxalobacteraceae;Massilia; 13 1 0 Proteobacteria;Betaproteobacteria;Burkholderiales;Oxalobacteraceae;Undibacterium; 2 0 0 Proteobacteria;Betaproteobacteria;Methylophilales;Methylophilaceae;Methylotenera; 3 1 8 Proteobacteria;Betaproteobacteria;Neisseriales;Neisseriaceae;uncultured; 3 0 0 Proteobacteria;Betaproteobacteria;Nitrosomonadales;Nitrosomonadaceae;Nitrosomonas; 0 1 0 Proteobacteria;Betaproteobacteria;NMD1; 5 0 0 Proteobacteria;Betaproteobacteria;Rhodocyclales;Rhodocyclaceae;12up; 5 0 0 Proteobacteria; Incertae Sedis;Order Incertae Sedis;Family Incertae Sedis;Candidatus Thiobios; 3 0 0 Proteobacteria;;Bdellovibrionales;Bacteriovoracaceae;Bacteriovorax; 0 2 0 Proteobacteria;Deltaproteobacteria;Bdellovibrionales;Bdellovibrionaceae;Bdellovibrio; 0 1 0 Proteobacteria;Deltaproteobacteria;;;Desulfocella; 1 0 0 Proteobacteria;Deltaproteobacteria;Myxococcales;0319-6G20; 0 4 0 Proteobacteria;Deltaproteobacteria;Myxococcales;mle1-27; 0 1 0 Proteobacteria;Deltaproteobacteria;Myxococcales;Sandaracinaceae;Sandaracinus; 0 1 0 Proteobacteria;Deltaproteobacteria;Myxococcales;uncultured; 1 2 0 Proteobacteria;Deltaproteobacteria;Order Incertae Sedis;Syntrophorhabdaceae;Syntrophorhabdus; 0 1 0 Proteobacteria;Deltaproteobacteria;Sva0485; 0 1 0 Proteobacteria;Deltaproteobacteria;Syntrophobacterales;Syntrophaceae;uncultured; 0 1 0 Proteobacteria;;Campylobacterales;Helicobacteraceae;uncultured; 1 0 1 Proteobacteria;;Enterobacteriales;;Escherichia-; 1 0 0 Proteobacteria;Gammaproteobacteria;Legionellales;Legionellaceae;Legionella; 0 8 0 Proteobacteria;Gammaproteobacteria;Pasteurellales;;Haemophilus; 17 0 0 Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Acinetobacter; 18 0 1 Proteobacteria;Gammaproteobacteria;Pseudomonadales;Moraxellaceae;Enhydrobacter; 4 0 0 Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas; 38 0 1 Proteobacteria;Gammaproteobacteria;;Nevskiaceae;Nevskia; 0 2 0 Proteobacteria;Gammaproteobacteria;Xanthomonadales;Solimonadaceae;uncultured; 0 2 0 Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae; 9 0 0 Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae;Arenimonas; 2 0 0 Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae;Stenotrophomonas; 3 9 4 Proteobacteria;TA18; 0 1 0 Spirochaetae;;Spirochaetales;;; 0 1 1

7 OTUs number Taxonomic Affiliation Surface microlayer Epilimnion Shared Spirochaetae;Spirochaetes;Spirochaetales;;; 0 1 0 Spirochaetae;Spirochaetes;Spirochaetales;Spirochaetaceae;uncultured; 0 1 0 ;BourFI; 0 2 0 Verrucomicrobia;Cl120-10; 15 6 13 Verrucomicrobia;FukuN18; 0 1 1 Verrucomicrobia;LD19; 0 2 0 Verrucomicrobia;OPB35 group; 0 11 0 Verrucomicrobia;Opitutae;Opitutales;Opitutaceae;Opitutus; 4 8 5 Verrucomicrobia;Opitutae;vadinHA64; 0 23 0 Verrucomicrobia;Spartobacteria;Chthoniobacterales;LD29; 0 2 0 Verrucomicrobia;Sta2-35; 0 3 2 Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;DEV007; 0 1 0 Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;; 1 2 3 Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Verrucomicrobiaceae;uncultured; 0 11 0 622 732 319

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Fig. S1. Rarefaction curves for the samples collected in the surface micro- layer (A) and the epilimnion (B) of Lake Pavin from May to August 2011.

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