Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

Table 1 Quality and quantity of extracted DNA, PCR amplicon, and HTS-read and amplicon sequence variant (ASV) count per sediment sample

Site	Code	Filter Type	Extracted DNA^a			Amplicon Library			Read Processing				Taxonomic Assignment
			Extracted DNA^a			qPCR (nM)^b	DNA Assay^c		Read Processing				Taxonomic Assignment
			ng/ul	A₂₆₀/A₂₈₀	A₂₆₀/A₂₃₀	qPCR (nM)^b	Size (bp)	Band	Raw Reads	Quality Filtered	Denoised	Non-Chimeric	Reads w/ Tax. ID	ASVs w/ Tax ID
A	ANP	NP	307.1	1.40	0.46	4.88	410	1	1,166,991	560,891	456,284	446,586	424,397	461
	A02	0.22	479.7	1.37	0.61	14.16	409	2	305,045	171,106	154,579	147,490	143,019	436
	A05	5	110.1	1.43	0.50	45.97	408	1	73,962	40,433	32,181	31,458	30,146	183
	A10	10	619.2	1.45	0.37	56.53	413	1	260,341	148,596	112,796	105,220	96,643	633
B	BNP	NP	625.5	1.45	0.30	56.79	413	1	446,984	135,890	87,857	86,948	85,109	75
	B02	0.22	397.9	1.61	0.75	27.33	414	1	79,771	29,699	22,339	22,153	20,745	104
	B05	5	44.3	2.53	0.06	8.34	415	1	146,808	101,535	86,288	82,169	77,590	465
	B10	10	35.8	3.08	0.04	17.38	415	1	182,665	135,387	125,620	112,804	105,066	1,071
C	CNP	NP	107.1	1.67	0.13	1.44	396	1	790,386	381,687	285,719	275,483	113,715	426
	C02	0.22	2.3	1.86	0.09	76.9	412	2	112,123	61,001	54,375	50,476	46,631	295
	C05	5	5.1	1.03	0.17	43.23	411	3	23,323	14,327	12,515	10,757	9,582	141
	C10	10	7.6	5.10	0.03	4.40	388	2	217,176	138,449	97,116	94,199	89,877	460
Total									3,805,575	1,919,001	1,527,669	1,465,743	1,242,520	2,875

^aInitial quantification and quality assessment of extracted DNA via NanoDrop Spectrophotometer
^bAmplicon library quantification via Kappa Illumina Library Quantification Kit
^cDNA Assay for fragment size quantification and quality via Agilent 2100 BioAnalyzer High Sensitivity DNA Kit. "NP" stands for non-processed sediment samples; "10" for the pre-filter (10 μm), "5" for the mid-filter (5 μm), and "0.22" for the collection filter (0.22 μm)

ISSN: 1471-2180