Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

Lammel, Daniel R.; Barth, Gabriel; Ovaskainen, Otso; Cruz, Leonardo M.; Zanatta, Josileia A.; Ryo, Masahiro; de Souza, Emanuel M.; Pedrosa, Fábio O.

doi:10.1186/s40168-018-0482-8

Table 2 Selection of the 15 most abundant OTUs (average of all samples) at genus level and potentially beneficial genera that correlated with pH and selected soil parameters (Spearman correlation, p, only significant values are shown, P < 0.05 and p > 0.4 or <− 0.4), and also the R² of the random forest (RF) models for the same parameters. The highest correlation values and RF-R² in each line, positive or negative, are depicted in bold (the full list of OTUs and their correlations is available in Additional file 6)

From: Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

OTU	Phylum	Genus	Frequency (%)	pH CaCl₂	Ca	Al	Fe	Cu	pH CaCl₂	Ca	Al	Fe	Cu
				(p)	(p)	(p)	(p)	(p)	(R²)	(R²)	(R²)	(R²)	(R²)
15 most abundant OTUs correlated with pH
OTU879	Proteobacteria	Variibacter	8.097	− 0.45		0.48	0.51		0.03		0.04	0.19	< 0.01
OTU812	Proteobacteria	Bradyrhizobium	2.938	− 0.49^a			0.51		0.02	< 0.01	0.05	0.23
OTU787	Proteobacteria	Uncultured	2.720	− 0.48		0.47	0.42		0.07	0.01	0.13	0.04
OTU290	Actinobacteria	Uncultured	2.507	− 0.60	− 0.48	0.63	0.55		0.16	0.03	0.15	0.12
OTU87	Acidobacteria	Uncultured	2.273	0.74	0.75	− 0.76		− 0.43	0.15	0.18	0.29	< 0.01	0.01
OTU35	Acidobacteria	Uncultured	2.224	− 0.80	− 0.77	0.80	0.46		0.19	0.22	0.19	0.02	< 0.01
OTU1353	Verrucomicrobia	C. xiphinematobacter	2.087	− 0.47		0.47			0.10	0.05	0.15	0.01	< 0.01
OTU1344	Verrucomicrobia	Uncultured	2.052	− 0.61	− 0.61	0.55		0.52	0.18	0.18	0.01		0.08
OTU1287	Proteobacteria	Acidibacter	1.795	− 0.65	− 0.65	0.63			0.15	0.10	0.15		0.02
OTU139	Actinobacteria	Acidothermus	1.763	− 0.57	− 0.46	0.62	0.61		0.19	0.03	0.13	0.15
OTU1117	Proteobacteria	Haliangium	1.676	0.56	0.50	− 0.53			0.16	0.06	0.15	< 0.01	< 0.01
OTU1342	Verrucomicrobia	Uncultured	1.662	− 0.71	− 0.67	0.66			0.14	0.12	0.13	0.01	< 0.01
OTU53	Acidobacteria	Uncultured	1.547	− 0.56	− 0.57	0.54		0.48	0.06	0.05	0.04	0.01	0.10
OTU84	Acidobacteria	Ambiguous_taxa	1.445	0.72	0.73	− 0.73		− 0.57	0.18	0.08	0.20		0.10
OTU287	Actinobacteria	Uncultured	1.283	− 0.53	− 0.42	0.53			0.11	0.05	0.13	0.03	0.01
Potentially beneficial genera^b
OTU858	Proteobacteria	Rhizobium	0.085	0.55	0.43	− 0.54	− 0.65		0.11	0.06	0.04	0.18
OTU852	Proteobacteria	Mesorhizobium	0.048	0.73	0.71	− 0.68	− 0.49	− 0.49	0.24	0.18	0.08	0.02	0.02
OTU1032	Proteobacteria	Herbaspirillum	0.003	− 0.52	− 0.47	0.51			0.11	0.08	0.08		< 0.01

^aWe reported Pearson (r) for Bradyrhizobium with pH, since it fitted better (full data in Additional file 6)
^bOTUs that may potentially promote plant growth [53, 54]

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ISSN: 2049-2618

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