Table 1. Genomes reconstructed from metagenomic-combined assembly.

Genome name	Environment	Genome size (bp)	Contigs	Genes	% of genome recovered (a/b)
Actinobacterium-149	Epilimnion	764 032	95	917	64/74
Nitrosomonadales-439	Epilimnion	996 711	125	1094	67/69
Polynucleobacter-567	Epilimnion	1 660 228	93	1777	72/62
Rickettsia-755	Epilimnion	1 013 290	136	1149	98/100
Betaproteobacteria-788	Epilimnion	990 006	133	1125	57/52
Methylophilaceae-913	Epilimnion	942 700	85	1111	76/99
Opitutae-1301	Epilimnion	2 036 179	101	1943	95/100
Opitutae-1800	Epilimnion	2 186 907	124	1,998	90/100
Actinobacterium-2057	Epilimnion	971 617	97	1063	74/58
Chlorobium-111	Hypolimnion	2 314 202	74	2319	92/100
Polynucleobacter-238	Hypolimnion	1 314 366	121	1475	66/52
Holophagales-254	Hypolimnion	2 981 798	188	2862	80/56
Desulfocapsa-433	Hypolimnion	3 073 408	152	2864	77/66
Methylotenera-545	Hypolimnion	1 431 993	51	1439	90/82
Actinobacterium-680	Hypolimnion	1 257 796	81	1353	73/60
Polynucleobacter-941	Hypolimnion	1 496 525	68	1581	57/54
TM7-1225	Hypolimnion	915 278	14	993	63/90
Methylobacter-1380	Hypolimnion	2 299 825	136	2072	68/59
Methylotenera-1381	Hypolimnion	1 077 715	49	1131	50/46
Sulfurimonas-1998	Hypolimnion	2 301 184	60	2383	98/100
Methylobacter-2062	Hypolimnion	3 124 798	188	2919	94/89
Bacteroidales-2086	Hypolimnion	3 680 027	151	2965	72/59
Actinobacterium-2152	Hypolimnion	845 311	113	980	61/64
Opitutae-2519	Hypolimnion	1 808 963	100	1654	72/88
Methylophilaceae-2902	Hypolimnion	1 002 927	75	1180	62/65
Desulfobulbus-2922	Hypolimnion	3 798 404	58	3387	93/92
Actinobacterium-3180	Hypolimnion	1 149 636	85	1251	67/54
Gallionella-3415	Hypolimnion	2 657 023	54	2637	97/95
Chlorobium-3520	Hypolimnion	2 156 671	83	2242	89/100
Acidomicrobium-3765	Hypolimnion	1 315 659	42	1392	76/94

a/b=Genome completeness estimated using the approaches of Parks et al. (2015) (a) and Rinke et al. (2013) (b).