TABLE 3.

Overview of important parameters for each sequencing run

	Before removing nonbacterial reads			After removing nonbacterial reads
Run	No. reads	No. reads pPNAa	No. reads mPNAb	No. reads	No. reads pPNAa	No. reads mPNAb	No. samples	No. taxac	Avg library size	% nonbacterial	Sample typesd	PCR conditions
Run 1	5E+06	4E+06	5E+05	9E+04	0	0	85	1,289	1,033	96.6	P	No clamps
Run 2	5E+05	6E+03	3E+05	6E+04	0	2	94	761	1,089	81.0	P	pPNA clamps
Run 3	1E+05	1E+03	3E+02	1E+05	0	0	12	142	9,487	3.29	I	No clamps
Run 4	8E+04	1E+03	2E+03	6E+04	0	0	58	761	1,114	39.6	P	pPNA and mPNA clamps
Run 5	1E+05	0E+00	0E+00	1E+04	0	0	7	377	20,569	0.0	I	No clamps

^aThe number of reads compatible with plastid peptide nucleic acid (pPNA) clamps.

^bMitochondrial peptide nucleic acid (mPNA) clamps.

^cNumber of different amplicon sequence variants (ASVs)

^dSample types included in the run (P = phyllosphere samples, I = invertebrate samples).