Table 3.

Qualified reads, OTU counts, and alpha diversity estimates of microbial populations^a

Sample ID	Bacteria						Archaea
	No. of qualified reads	OTU count	No. of observed species	Chao1 index	Shannon index	Simpson indexb	No. of qualified reads	OTU count	No. of observed species	Chao1 index	Shannon index	Simpson indexb
DIS-NDW	22,309	2,031	2,024.000	2,759.10	7.68	0.971	3,757	102	101.900	125.906	3.500	0.828
DIS-BWI	23,515	1,828	1,827.500	2,673.23	6.67	0.957	357	126	72.400	95.796	4.718	0.911
DIS-LCL	19,545	2,297	2,295.500	3,080.16	8.53	0.989	1,359	110	109.900	219.150	5.083	0.937
ATL-NDW	18,787	1,816	1,808.300	2,643.19	7.93	0.981	3,299	97	97.000	171.000	3.654	0.853
ATL-BWI	22,578	2,117	2,116.700	3,095.92	7.93	0.985	7,356	130	130.000	164.731	3.269	0.798
ATL-UCL1	18,925	1,959	1,953.500	2,664.68	8.33	0.990	955	93	92.900	146.564	5.065	0.944
ATL-UCL2	16,737	2,169	2,166.800	2,994.93	8.40	0.987	1,145	101	100.700	151.184	4.862	0.936
ATL-LCL	20,474	2,299	2,298.700	2,934.74	8.38	0.985	639	71	70.000	109.985	4.648	0.932

^aSamples were rarefied at the smallest libraries, and results were averaged over 100 repetitions. In Atlantis II, all metrics more or less agree that bacteria and archaea have higher diversity in transition zones and the brine layers than in normal deep water. In Discovery, the LCL was consistently the highest in diversity for bacteria and archaea, followed by NDW and then BWI (with some differences between species richness and diversity indices). The number of unclassified reads was 10,600.

^bThe Simpson index used here is the Gini-Simpson index.