Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient Item Type Article Authors Hough, Moira; McClure, Amelia; Bolduc, Benjamin; Dorrepaal, Ellen; Saleska, Scott; Klepac-Ceraj, Vanja; Rich, Virginia Citation Hough, M., McClure, A., Bolduc, B., Dorrepaal, E., Saleska, S., Klepac-Ceraj, V., & Rich, V. (2020). Biotic and environmental drivers of plant microbiomes across a permafrost thaw gradient. Frontiers in Microbiology, 11, 796. DOI 10.3389/fmicb.2020.00796 Publisher FRONTIERS MEDIA SA Journal FRONTIERS IN MICROBIOLOGY Rights Copyright © 2020 Hough, McClure, Bolduc, Dorrepaal, Saleska, Klepac-Ceraj and Rich. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Download date 25/09/2021 11:20:15 Item License https://creativecommons.org/licenses/by/4.0/ Version Final published version Link to Item http://hdl.handle.net/10150/649227 Supplemental Tables Table S1: Taxonomy of keystone OTUs (those in the 99th percentile of importance for a network and networks in which they attained this level of importance). Functional OTU Domain Phylum Class Order Family Genus Phyllosphere Rhizosphere Peat Habitat Group 12 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Sinobacteraceae C. rotundata Bog A.polifolia, 14 Bacteria Acidobacteria DA052 Ellin6513 A. polifolia E.vaginatum Palsa 15 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidocella Sphagnum sp Palsa 16 Bacteria Acidobacteria Holophagae Holophagales Holophagaceae E. vaginatum (bog) E. angustifolium (fen) Bog/Fen 21 Bacteria Proteobacteria Betaproteobacteria SBla14 A. polifolia Bog C. rotundata 22 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Methylocystaceae (bog) A. polifolia (bog) C. rotundata (fen) Bog/Fen Methanotroph E. angustifolium 23 Bacteria Verrucomicrobia [Pedosphaerae] [Pedosphaerales] auto67 (fen) E. vaginatum (bog) Bog/Fen A.polifolia (bog), 24 Bacteria Acidobacteria DA052 Ellin6513 Sphagnum sp (palsa) E.vaginatum (bog) Bog/Palsa R.chamaemorus, 25 Bacteria Bacteroidetes [Saprospirae] [Saprospirales] Chitinophagaceae E.vaginatum Palsa 31 Bacteria Bacteroidetes Bacteroidia Bacteroidales C. rotundata Fen C. rotundata (bog), 32 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae E.angustifolium (fen) Bog/Fen A. polifolia (bog, A. polifolia (palsa), E. 35 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae palsa) vaginatum (bog) Palsa/Bog 36 Archaea Euryarchaeota Methanobacteria Methanobacteriales Methanobacteriaceae Methanobacterium E. vaginatum Bog Methanogen E. vaginatum 39 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. vaginatum (palsa) (palsa,bog) Palsa/Bog R.chamaemorus(palsa), 40 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Bradyrhizobium E.angustifolim (fen) Palsa/Fen R.chamaemorus (palsa), 41 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Burkholderiaceae Burkholderia A.polifolia (bog) Palsa/Bog A.polifolia (bog), 43 Bacteria Actinobacteria Actinobacteria Actinomycetales A.polifolia (palsa) E.vaginatum (bog) Palsa/Bog 46 Bacteria Armatimonadetes Armatimonadia FW68 Sphagnum sp C.rotundata Bog 48 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidocella Sphagnum sp Palsa/Bog C. rotundata, 53 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Koribacteraceae Candidatus Koribacter E.angustifolium Fen 54 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Rhodoferax C. rotundata Fen Sphagnum sp (palsa), 55 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Koribacteraceae A. polifolia (bog) Palsa/Bog 58 Bacteria Proteobacteria Gammaproteobacteria Xanthomonadales Sinobacteraceae Sphagnum sp Palsa E. vaginatum R. chamaemorus 59 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae (bog) A. polifolia (palsa) (palsa) Palsa/Bog 61 Bacteria WPS-2 E. vaginatum Bog 62 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Paludibacter E. angustifolium Fen 63 Bacteria Acidobacteria Holophagae Holophagales Holophagaceae Geothrix C. rotundata (fen) C. rotundata (bog) Bog/Fen 66 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Koribacteraceae E. vaginatum Bog 70 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. vaginatum Palsa A.polifolia (palsa), C. 72 Bacteria Verrucomicrobia [Methylacidiphilae] Methylacidiphilales rotundata (bog) Palsa/Bog Methanotroph 73 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acidocella C. rotundata Bog 78 Bacteria Bacteroidetes [Saprospirae] [Saprospirales] Chitinophagaceae E. vaginatum Palsa A. polifolia, R. chamaemorus, E. 90 Bacteria Acidobacteria DA052 Ellin6513 vaginatum Palsa 104 Bacteria Actinobacteria Actinobacteria Actinomycetales Intrasporangiaceae E. angustifolium Fen C. rotundata, 105 Bacteria Fibrobacteres E.angustifolium Fen 110 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Sphagnum sp Bog 117 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. vaginatum Bog 120 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae Sphagnum sp Palsa 123 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia A. polifolia Bog 125 Bacteria Bacteroidetes [Saprospirae] [Saprospirales] Chitinophagaceae A. polifolia Bog 128 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. angustifolium C. rotundata Fen 133 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae Sphagnum sp Palsa 136 Bacteria Acidobacteria Solibacteres Solibacterales Sphagnum sp Palsa 137 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae A. polifolia Bog E.vaginatum (palsa), 145 Bacteria Actinobacteria Acidimicrobiia Acidimicrobiales Sphagnum sp (bog) Palsa/Bog 146 Bacteria Proteobacteria Deltaproteobacteria Myxococcales C. rotundata Fen A. polifolia, 167 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Methylocystaceae E.vaginatum Palsa Methanotroph A.polifolia, E.vaginatum, 171 Bacteria Proteobacteria Gammaproteobacteria Methylococcales Sphagnum sp Bog 178 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Koribacteraceae R. chamaemorus Palsa 197 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae E. vaginatum Palsa 200 Bacteria Verrucomicrobia [Pedosphaerae] [Pedosphaerales] auto67 C. rotundata Bog 203 Bacteria Proteobacteria Deltaproteobacteria Desulfuromonadales Geobacteraceae Geobacter E. vaginatum Bog 246 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Paludibacter Sphagnum sp Bog 264 Bacteria Chloroflexi Ellin6529 C. rotundata Fen C. rotundata (bog), 274 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae Edaphobacter E.angustifolium (fen) Bog/Fen 306 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. vaginatum Palsa 311 Bacteria Bacteroidetes Bacteroidia Bacteroidales C. rotundata Fen 320 Bacteria Proteobacteria Gammaproteobacteria Methylococcales Crenotrichaceae Crenothrix E. angustifolium Fen Methanotroph 371 Bacteria Bacteroidetes Cytophagia Cytophagales Cytophagaceae Hymenobacter C. rotundata Fen 390 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. vaginatum Bog 489 Bacteria Proteobacteria Deltaproteobacteria Myxococcales E. angustifolium Fen 505 Bacteria Acidobacteria Solibacteres Solibacterales Solibacteraceae Candidatus Solibacter C. rotundata Fen 530 Bacteria Proteobacteria Alphaproteobacteria A. polifolia Bog 590 Bacteria Actinobacteria Thermoleophilia Gaiellales C. rotundata Fen 732 Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Paludibacter C. rotundata Bog 737 Bacteria Actinobacteria Actinobacteria Actinomycetales Nakamurellaceae C. rotundata Fen 772 Bacteria Proteobacteria E. angustifolium Fen 985 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae C. rotundata Bog 3373 Bacteria Verrucomicrobia Opitutae Opitutales Opitutaceae Opitutus A. polifolia Bog 3519 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae E. angustifolium Fen 5321 Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae Chromobacterium C. rotundata Bog 5950 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae A. polifolia Bog 7027 Bacteria Acidobacteria Acidobacteriia Acidobacteriales Acidobacteriaceae Sphagnum sp Bog 9433 Bacteria Verrucomicrobia [Pedosphaerae] [Pedosphaerales] auto67 C. rotundata Bog Table S2: Number of keystone OTUs found in each network type Phyllosphere Rhizosphere Peat Palsa A. polifolia 2 4 3 R. chamaemorus 3 - 4 E. vaginatum 2 4 5 Sphagnum sp 3 4 - Bog A. polifolia 4 5 5 C. rotundata 2 5 6 E. vaginatum 2 5 7 Sphagnum sp 2 5 - Fen C. rotundata 3 5 6 E. angustifolium 3 6 5 Table S3: Putative methanotrophs Domain Phylum Class Order Family Genus Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Other Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Beijerinckiaceae Beijerinckia Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae unknown Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Devosia Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Hyphomicrobium Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Hyphomicrobiaceae Rhodoplanes Bacteria Proteobacteria Alphaproteobacteria