TABLE 1.

Overview of the mapping rates of the N removal genes to the Kaiju database to reveal possible key players (top 12 phyla) for the significantly different gene families plus nirS^a

Organism(s)	Nitrification for amoABC, nxrB		Denitrification (DNRA)				DNRA for nrfCD		Denitrification						Anammox for hzo, hszA		ANRA for nirA		N_fixation for nifHK		Others for hcp
			napA		narH				nirK		nirS		nosZ
	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR	BAL	SAR
Acidobacteria			2	12	6	6	119	18	2	12	2	14	13	11	2		2	1	6		4
Actinobacteria			5		6	7	13	4	6	8	2	1	4	3			3	6			1
Alphaproteobacteria b			2	4	2	34	25	9	7	22	3	8	5	19			8	32	11	2	2
Bacteroidetes			19	1	5		364	20	52	8	15		140	54	4		7	4	16	3	8
Chlorobi			1				106	11	10		6		22
Chloroflexi			17	14	3		26	38	31	113	15	1	51	37			6	11	2	4	11
Deltaproteobacteria c	71	12	217	19	84	11	526	102	14	5	116	25	115	37			20		74	9	285	20
Euryarchaeota					1		20		3		10	4	1				8		149		31
Gammaproteobacteria d	28	45	105	63	86	142	669	432	86	87	448	211	158	49			119	106	71	37	8
Nitrospirae	9	300	3	9			38	10	1	157		65					1	30	1	13	1
Planctomycetes			1	6			2		9	22	16		13	5	11				6		8	3
Verrucomicrobia			27	6	10		26	39	10	45	11	5	14	32	1		7	17	5		6

^aThe numbers are the sum of gpm per gene per lake and phyla. The most abundant phyla are highlighted in boldface for Lake Baldegg and underlining for Lake Sarnen. The most abundant classes of the Proteobacteria are listed in the footnotes below. The full list of Proteobacteria orders per gene can be found in Table S5. Note that Gammaproteobacteria include Betaproteobacteria.

^bThe most assigned orders of Alphaproteobacteria were Caulobacterales (most often assigned in Lake Sarnen), Rhizobiales, Rhodobacterales (most often assigned in Lake Sarnen), and Rhodosprillales.

^cThe most abundant orders of Deltaproteobacteria were Desulfobacterales, Desulfuromonoadales, and Syntrophobacterales.

^dThe most often assigned Gammaproteobacteria (including Betaproteobacteria) orders were Acidiferrobacterales (most often assigned in Lake Sarnen), Aeromonadales (most often assigned in Lake Sarnen), Chromatiales, Enterobacterales (most abundant in Lake Baldegg), Methylococcales, Tiotrichales (most abundant in Lake Baldegg), Burkolderiales, Nitrosmonadales, and Rhodocyclales.