Global patterns in bacterial diversity

Lozupone and Knight. 10.1073/pnas.0611525104.

Supporting Information

Files in this Data Supplement:

SI Data Set 1
SI Figure 4
SI Figure 5
SI Text

SI Figure 4

Fig. 4. UniFrac UPGMA cluster. The results of clustering the 202 samples by using a UniFrac distance matrix and the UPGMA algorithm. The nonsaline environments form a monophyletic clade (denoted with two blue stars) that separates them from the saline environments. The branches are colored by environment type with the following colors: Nc, yellow; Nso, light green; Nsu, red; Nse, purple; Nw, blue; Nen, salmon; Nsp,: brown; Sc, yellow; Sse, orange; Swa, bright green; Swb, dark blue; Sws, cyan; Smi, light purple; So, hot pink; M, black. The groups indicated by boxes on the right (and a red star for the clade where applicable) are described in more detail below. A file with the sample names associated with each branch ("UPGMA_results.html") is also provided. A, saline sediment, anoxic water, and misc other: Two hydrothermal sediments from the Saline sediment (Sse) group (Sse_Mh_42, Sse_Mh_18), anoxic water (Swa_M_32, Swa_M_33), and members of the Saline-Misc group (So) including hypersaline microbial mats (So_Mm+_166-8) and hydrothermal vent colonizers (So_Hc_19, So_Hc_128). B, Subsurface and open ocean water: All members of the Saline water submerged (Swb) group except for Swb_M_130 (which groups with the surface water) and two members of Saline water surface (Sws) group, Sws_M_83 and Sws_M_163. C, Saline sediment, anoxic water, and misc other: Diverse samples from the Saline sediment (Sse) group, five samples from anoxic hypersaline basins in the Mediterranean Sea (Swa group), and a couple of members of the Saline-Misc group (So). D, Saline sediment and misc other: Diverse samples from the Saline sediment (Sse) group and from the Saline-Misc group (So) including all four stromatolite samples, formations in a cave flooded with saline groundwater (So_36), basalt from the seafloor (So_En_135), and salt march grass (So_Mc_72). E, Saline sediment/anoxic: Mostly sediments but also anoxic water from a saline lake (Swa_L+_59). F, Coastal surface water: Most members of the Saline water surface (Sws) group, two estuary water samples (M_w_200, M_w_201), and one member of the Saline water subsurface (Swb) group (Swb_M_130) form a clade with the Saline Cultured (Sc) group members. G, Saline-cultured and Marine Ice: All but one member of the Saline Cultured (Sc) group (Sc_Mr+_84, from a stromatolite, groups closer to the uncultured stromatolite samples) and all members of the Marine Ice (Smi) group. H, Misc and submerged soils: Miscellaneous members of the soil (Nso) group and most member of the Non-saline submerged (Nsu) group including wetlands, aquifers, and a rice paddy. I, Nonsaline sediment: All members of the Nonsaline sediment (Nse) group. J, Soil: Most members of the soils (Nso) group. K, Rock and Cave: Members of the Nonsaline endolithic group (Nen), two of four from caves, and sediment from aphotic wind cave in South Dakota (N_su_c_188). L, Misc nonsaline: Miscellaneous members of the Nonsaline endolithic (Nen), Soil (Nso), and submerged soils (Nsu) groups, that group in a clade with members of the Nonsaline cultured (Nc) group, including extremely acidic rocks in Yellowstone National Park (Nen_100) and PCB contaminated soils (Nso_p_23, Nso_p_34). M, Nonsaline cultured: Members of the Nonsaline cultured (Nc) group that were cultured from soils, sediments, and air. One member of the Nonsaline endolithic (Nen) group (Nen_110) N: Lakes and Rivers: All samples in the Nonsaline water (Nw) group, all lake samples in the Nonsaline-cultured (Nc) group, one estuary (M_w_11), and one Saline water-surface sample (Sws_M_13). Sws_M_13 was likely pulled into this group because it is from a single study that sequenced from a river, estuary, and adjacent coastal ocean, which all group in this clade. O, Hotsprings: All hotsprings in the Nonsaline springs (Nsp) group and an intertidal hotspring (M_sp_101) from the Mixed (M) group.

SI Figure 5

Fig. 5. Phylogenetic diversity (PD) regression analysis. Plot of the amount of branch length that remains in the phylogenetic tree when only sequences from a particular sample is included (PD), vs. the number of OTUs that represents each sample. Bacteria that were cultured from nonsaline environments (Nc, pink circles) generally fell below the main regression line (blue), thus having lower phylogenetic diversity. Saline sediments (purple circles) generally fell above the main regression line.

Data Set 1. Information on the environmental samples that are included in the survey

Name	Description	# SEQ	# OTU	G Resid	PD Resid	Ref
M_sp_101	Intertidal hotsprings on the coast of the Reykjanes peninsula in northwest Iceland (45-95C)	38	33	0.206	1.145	1
M_w_11	Columbia River Estuary, Oregon,	119	82	-0.785	1.293	2
M_w_200	Station N1 of the Portuguese estuary Ria de Aveiro representing a deep marine zone	32	31	-0.474	-0.914	3
M_w_201	Station I6 of the Portuguese estuary Ria de Aveiro representing a shallow brackish zone	25	24	-0.261	-0.318	3
Nc_ai_132	Aerosolized bacteria from desert dust events in Mali, West Africa (cultured)	95	48	-0.874	-3.051	4
Nc_Ls_97	Cultured from sediment from shallow, eutrophic Lake Kasumigaura in Japan	210	66	-0.772	-0.555	5
Nc_Lw_113	Cultured from water from small, shallow, eutrophic lake Zwischenahner Meer in Northern Germany	43	24	-0.418	-0.746	6
Nc_Lw_114	Cultured from water from mesotrophic prealpine lake Starnberger, Southern Bavaria, Germany	36	23	-0.399	-0.817	6
Nc_Lw_115	Cultured from water from oligotrophic alpine lake Walchensee, Southern Bavaria, Germany	33	16	-0.349	-1.118	6
Nc_so_186	Cultured from sand from the desert of Tataouine (south Tunisia)	40	25	-0.235	-1.481	7
Nc_so_39	Cultured from no-tilled agricultural soil in Athens, Georgia	73	59	-1.253	-3.034	8
Nc_so_40	Cultured from an earthworm burrow in no-tilled agricultural soil in Athens, Georgia	26	21	-0.431	-1.628	8
Nc_so_73	Cultured from a grass pasture soil in Victoria. England	350	95	-1.488	-2.729	9
Nc_so_82	Cultured from a pasture soil in Victoria, Australia	89	46	-0.899	-1.881	10
Nc_so_95	Cultured from a pasture soil from Victoria, Australia	258	122	-2.531	-3.393	11
Nen_100	Extremely acidic (pH 1) rocks in the geothermal environment of Yellowstone National Park	65	42	0.618	0.913	12
Nen_110	Wall of aphotic, oligotrophic Fairy Cave in Colorado (U.S.A.)	37	31	0.189	-0.419	13
Nen_126	Wall of aphotic La Garma Cave, northern Spain	58	39	-0.327	-0.456	14
Nen_127	Wall of artificially lighted Llonin Cave, northern Spain	27	17	0.120	-0.595	14
Nen_192	Epilithic bacterial community in Limestone from a Maya archaeological site in Yucatan Mexico	54	49	0.699	1.527	15
Nen_193	Endolithic bacterial community in Limestone from a Maya archaeological site in Yucatan Mexico	30	28	0.087	-0.590	15
Nen_45	Wall of artificially lighted Tito Bustillo cave, Spain	41	33	0.025	-0.119	16
Nse_L_149	Sediment from Rainbow Bay, an acidic, mesotrophic freshwater pond on the Carolina coastal plain (U.S.A.)	33	31	0.392	-0.417	17
Nse_L_150	Sediment from oligotrophic, acidic Muldenberg reservoir, Saxony Germany	164	142	0.727	2.449	18
Nse_L_151	Sediment from oligotrophic Neuzehnhain rezervoir, Saxony Germany	158	137	0.302	1.542	18
Nse_L_152	Sediment from highly eutrophic Quitzdorf rezervoir, Saxony Germany	145	133	1.618	4.013	18
Nse_L_153	Sediment from mesotrophic Saidenbach rezervoir, Saxony Germany	147	128	1.498	4.022	18
Nse_L_198	Sediment of freshwater Lake Washington (60m depth)	104	54	-0.476	0.473	19
Nse_L_98	Sediment from shallow, eutrophic Lake Kasumigaura in Japan	112	83	0.133	0.371	5
Nso_10	Rhizosphere samples from fertilized and reseeded grass pasture soils in Scotland	137	116	-1.276	0.831	20
Nso_106	Light, sandy loam soil in arid northern Arizona, U.S.A.	254	200	0.173	0.139	21, 22
Nso_107	Coarse textured, well-drained cinder soil in arid northern Arizona U.S.A.	286	182	-0.574	-0.696	21, 22
Nso_108	Agricultural soil in Wisconsin U.S.A.	526	351	-1.406	-3.027	23
Nso_116	Rhizosphere of lodgepole pine seedlings in Williams Lake, British Columbia	226	179	-2.330	-1.047	24
Nso_117	Rhizosphere of lodgepole pine seedlings in Smithers, British Columbia	211	170	-2.142	-1.025	24
Nso_118	Rhizosphere of lodgepole pine seedlings in Prince George, British Columbia	217	160	-2.388	-0.996	24
Nso_158	Sandy soil in Virginia, U.S.A.	67	48	-0.479	0.480	25
Nso_159	Sandy soil in Delaware, U.S.A.	75	46	0.072	-0.392	25
Nso_185	Sand from the desert of Tataouine (south Tunisia)	117	91	0.133	0.882	7
Nso_190	Loamy-sand soil from a chaparral ecosystem in San Diego, California U.S.A.	126	92	-0.475	0.264	26
Nso_199	Soil from exotic pine plantations of subtropical Australia under different residue management regimes	314	190	-1.103	-3.392	27
Nso_202	Silt loam soil from a century-old manure treated agroecosystem in Oklahoma, U.S.A.	94	61	-0.375	0.646	28
Nso_3	Agricultural soil in Wisconsin, U.S.A.	120	116	0.198	-0.665	29
Nso_4	Mature forest and active pasture soils in Para State Brazil	99	86	0.851	1.214	30
Nso_41	No-tilled agricultural soil in Athens, Georgia	95	84	0.200	1.744	8
Nso_46	Forest soil in British Columbia after whole tree harvesting with no soil compaction	280	205	-2.050	-0.853	31
Nso_47	Forest soil in British Columbia after whole tree harvesting and surface organic matter removal	140	118	-1.291	0.579	31
Nso_65	Uncultivated agricultural soil in Wisconsin	318	249	-0.852	-4.308	32
Nso_79	Tropical grass pasture soil under Acacia trees in Senegal (Dry season)	49	33	0.210	0.049	33
Nso_80	Tropical grass pasture soil under Acacia trees in Senegal (Rainy season)	68	32	-0.495	-1.030	33
Nso_81	Alpine dry meadow soils in the Colorado Rocky Mountains	159	121	-0.747	-0.974	34
Nso_86	Soil from Kolmberg, an oak-hornbeam forest in the eastern part of Austria	46	41	-0.717	0.242	35
Nso_87	Soil from Rothwald, a spruce-fir-beach forest in the eastern part of Austria	50	41	-0.703	-0.492	35
Nso_88	Soil from Stampfital, an Austrian pine forest in the eastern part of Austria	41	35	-0.539	-0.877	35
Nso_9	Rhizosphere samples from natural grass pasture soils in Scotland	138	118	-1.468	0.078	20
Nso_96	Loamy sand soil from Dunnwald forest in the suburban area of Cologne, Germany (pH 3.9)	135	48	-0.362	-2.193	36
Nso_l_44	Leaf litter from a pine forest in central Java, Indonesia	87	62	-0.040	0.026	37
Nso_p_23	PCB-polluted soil collected near Wittenberg, Germany	123	73	-0.632	-0.765	38
Nso_p_34	PCB-polluted soil collected near Wittenberg, Germany	173	48	-0.819	-1.018	39
Nso_p_67	Heavy metal-contaminated rhizosphere of a metal-hyperaccululating plant and contaminated bulk soil	282	164	-2.056	-2.229	40
Nsp_1	Sediment from Bor Khlueng hot spring in Ratchaburi province, Thailand (50-57C)	38	32	0.533	0.829	41
Nsp_7	Sediment from Obsidian Pool hot spring, Yellowstone National Park U.S.A. (75-95C)	129	53	1.113	1.342	42
Nsp_93	Obsidian Pool Prime hot spring, Yellowstone National Park U.S.A. (74C) - colonized growth slide	181	19	0.025	-0.826	43
Nsp_94	Queen's Laundry hot spring, Yellowstone National Park U.S.A. (89C) - colonized growth slide	17