Table 2. Read numbers and statistics.

Sample	Readsa	% rRNAb	Non-rRNA reads
			Replicatesc	nr Hitsd	KEGG hitsd
Santa Cruz wharf: vacuum	179 643	80%	20%	17 988	15 869
Santa Cruz wharf: ESP	160 364	82%	18%	14 702	12 850
Station M1: peristaltic pump	118 595	41%	26%	20 981	18 677
Station M1: ESP	203 574	42%	11%	41 295	37 086
0500 hours rRNA-subtracted	248 016	33%	4%	82 387	69 157
0500 hours unsubtracted	298 380	91%	7%	11 802	10 089
1000 hours rRNA-subtracted	102 024	40%	17%	25 197	22 250
1000 hours unsubtracted	149 186	82%	27%	9979	8612
1800 hours rRNA-subtracted	238 635	38%	17%	54 040	46 253
1800 hours Unsubtracted	232 248	83%	12%	15 694	13 156
2200 hours rRNA-subtracted	235 339	35%	13%	52 069	43 956
2200 hours unsubtracted	202 650	82%	24%	10 701	8890
DNAe	1 535 834	0.4%	0.97%	1 035 676	956 510

Abbreviations: KEGG, Kyoto Encyclopedia of Genes and Genomes; nr, non-redundant; rRNA, ribosomal RNA.

^aTotal number of sequence reads passing quality filters.

^bPercentage of total pyrosequencing reads with significant (bitscore > 50) BLASTN hits to prokaryotic and eukaryotic rRNA (16S, 18S, 23S, 28S, 5S).

^cPercentage on non-rRNA reads identified as artificial replicates (99% identity, 1-bp length difference) and removed.

^dNon-replicate, non-rRNA reads with significant (bitscore > 50) BLASTX hits to proteins in the NCBI nr or KEGG Genes databases.

^eMetagenomic data set, sequenced using GS FLX Titanium chemistry rather than GS FLX.