TABLE 3.

Number of reads and operational taxonomic units (OTUs) derived from NGS analysis of xylem sap microbiota from DNA samples extracted with 12 extraction protocols, amplified with the 967F + 1193R primer pair (PCR2), and taxonomic assignment using the Greengenes 13-8 and Silva 132 reference databases.

Reads/OTU numbers		Norgen	Norgen	Pure	Quick	Power	Power	Power	Nucleo	Nucleo	Canvax	Canvax
		MicrobiomeV1	MicrobiomeV2	Link	Pick	Soil	Lyzer	Plant	Nucleo	SpinPL2	Soil	Tissue	CTAB*
Number of reads (Mean/sample)		4,586	5,888	3,931	4,977	4,724	4,502	3,265	3,828	4,731	5,777	4,090	3,821
Greengenes	Unassigned Reads (%)	15	11	8	12	13	8	11	46	21	5	13	6
	Plant (chloroplast + mitochondria) reads (%)	33	70	79	18	18	3	28	2	4	59	36	14
	Bacterial reads (%)	52	19	13	70	69	89	61	52	75	36	51	80
	OTUs at the Phylum level	7	6	4	7	7	8	7	8	7	6	5	8
	OTUs at the Class level	14	7	6	12	9	14	13	12	14	10	7	12
	OTUs at the Order level	25	10	12	24	16	24	21	26	28	18	12	19
	OTUs at the Family level	42	17	19	48	34	49	41	56	58	42	30	35
	OTUs at the Genus level	51	24	21	66	41	75	54	81	77	55	32	45
	Total Assigned OTUs	56	24	21	73	50	90	63	91	88	62	35	47
	Unassigned Reads (%)	15	11	8	11	13	7	11	46	21	5	13	6
Silva	Plant (chloroplast + mitochondria) reads (%)	33	70	79	18	18	3	28	2	4	59	36	14
	Bacterial reads (%)	52	19	13	71	69	90	61	52	75	36	51	80
	OTUs at the Phylum level	8	6	4	8	8	10	8	9	9	6	6	9
	OTUs at the Class level	16	7	6	14	11	17	15	14	19	10	9	14
	OTUs at the Order level	31	15	14	30	20	30	28	32	37	21	16	23
	OTUs at the Family level	47	21	19	49	35	52	42	52	60	39	30	39
	OTUs at the Genus level	60	28	21	67	45	80	58	78	82	54	33	49
	Total Assigned OTUs	64	29	21	74	49	93	65	84	91	61	35	52

CTAB, cetyltrimethylammonium bromide.