Table 2.

Differences in the number of putative fungal functional groups (identified by FUNGuild “trophic level” annotations) in the rhizosphere of healthy and diseased cotton plants in two cultivars (LM28 and ZHM2).

Annotated		LM28			ZHM2			Both
		Sig.	Odds ratio	P	Sig.	Odds ratio	P	Sig.	Odds ratio	P
Unknown	2,190	283	1.38	<0.001	394	1.22	0.004	462	1.21	0.003
Sapa	543	156	0.62	<0.001	190	0.63	0.000	199	0.7	<0.001
Pathb	82	14	1.04	1.000	14	1.29	0.500	19	1.1	0.803
Symc	83	5	2.96	0.010	9	2.03	0.039	12	1.77	0.070
Sap-Path	85	22	0.69	0.133	23	0.81	0.376	29	0.75	0.195
Sap-Sym	72	16	0.80	0.452	21	0.75	0.275	22	0.84	0.440
Path-Sym	26	6	0.77	0.618	6	0.95	0.820	7	0.95	0.830
Sap-Path-Sym	268	95	0.50	<0.001	79	0.75	0.030	105	0.65	0.001

Individual OTUs with significant differences in its abundance between diseased and healthy plants determined by DESeq2 analysis. Odds ratio of <1 indicates a higher proportion of OTUs in the particular fungal functional group in the microbiome of diseased samples, and P-value indicates whether the odds ratio differs significantly from 1.0.

^aSaprotroph, ^bPathotroph, ^cSymbiotroph.