Table 1. Number of sequences (no. seq) and the diversity estimates from partial 16S rRNA gene fractions (∼700 bp) and the related ITS fragments (∼400 bp) of clone libraries used in this study.

		16S rRNA gene fraction				ITS fraction
Transect (T)a	No. seq	OTUs	Chao1b	(1/D)c	% GECd	OTUs	Chao1b	(1/D)c	% GECd	DivITS/Div16S e
Surface (10 m)
T1_C	159	6	7–43	1.93	98	110	225–522	124	47	18.3
T1_OP	154	7	7–30	2.12	97	119	276–658	203	37	17.0
T2_C	165	7	7–30	1.97	98	129	342–871	246	36	18.4
T2_OP	135	5	5–29	1.88	98	113	300–798	302	28	22.6
T3_C	153	5	5–13	2.11	99	107	176–341	159	50	21.4
T3_OP	141	10	17–115	1.86	94	118	411–1326	260	26	11.8
T4_C	168	6	7–43	1.84	98	139	488–1428	298	27	23.2
T4_OP	121	7	9–59	1.61	96	109	438–1628	484	17	15.6
T5_OP	136	10	17–115	1.90	94	90	186–488	94	49	9.0
T6_C	154	8	11–76	1.42	96	111	274–718	117	41	13.9
T6_OP	109	5	5–29	1.23	97	69	154–503	39	49	13.8
Water column
50 m	247	8	8–14	2.20	99	128	200–368	106	68	16.0
200 m	218	36	42–93	5.71	91	134	231–436	121	57	3.7
700 m	144	26	43–242	5.82	89	62	80–173	45	78	2.4
1500 m	142	29	42–186	9.66	88	80	134–320	61	61	2.8

Operational taxonomic units (OTUs) defined at a 3% distance threshold.

^aThe letters “C” or “OP” after the transect number (i.e., T1_#) denote coast and open ocean environments, respectively (details in Table S1).

^bRanges of estimated richness indices are reported as the 95% confidence interval.

^cSimpson’s Reciprocal Index; higher values of this index indicate a highly diverse community.

^dGood’s estimated coverage provides information of how large a fraction of the OTUs have been sampled more than once.

^eThe ratio between the number of OTUs observed within ITS sequences (Div_ITS) and that of the 16S rRNA gene fractions (Div_16S).