TABLE 1 .

Prochlorococcus metabolic pathways with transcripts that were consistently depleted during the first 5 h of extended darkness^a

Condition and pathwayb	Transcripts in pathway exhibiting significant differential depletion	P valuec
Depleted in both axenic cultures and coculture
Chemoautotrophic energy metabolism	ctaC, ctaD, ctaE, spt	2.1E−02
CO2 fixation	cbbA, gapA, glxK, pgk, rbcL, rbcS, tktA	1.2E−02
Generation of precursor metabolites and energy	aspC, cbbA, ctaC, ctaD, ctaE, eno, gap2, gapA, glk, gltA, glxK, gpmI, gnd, mqo, ndhE, ndhI, petH, pgk pgl, ppc, pta, rbcS, rbcL, spt, tktA, ubiA, zwf, PMN2A_0452, PMN2A_1511	9.8E−03
Glycogen degradation	glgP, malQ, pgm	8.8E−02
Nucleoside and nucleotide biosynthesis	apt, atpA, atpB, atpC, atpD, atpE, atpF, atpG, atpH, carA, cca, codA, dcd, glxK, guaA, guaB, ndk, nrdA, purE, purH, purK, purL, purM, purS, purT, pyrB, pyrC, pyrD, queA, thyX, tmk, rnpA, upp, PMN2A_0984, PMN2A_1284	1.6E−03
Oxidative pentose phosphate pathway	gnd, pgl, zwf, tktA	6.0E−03
Depleted only in axenic cultures
Cob(II)yrinate a,c-diamide biosynthesis	cbiD, cobB, cobI, cobK, cobM, cobN, cysG	2.0E−02
l-Isoleucine biosynthesis	aspC, ilvA, ilvB ilvD, ilvE, lysC thrA, PMN2A_1138	3.0E−02
Homoserine and methionine biosynthesis	aspC, lysC, met3, met17, metA, metB, thrA, PMN2A_1269, PMN2A_1748	1.0E−02
NAD metabolism	nadB, nadD, nadE, pntA, pntA-2, pntB, ppnK	2.0E−02
Other amino acid biosynthesis	argC, lysC, met17, thrA, PMN2A_1832	8.0E−02
Polymer/polysaccharide degradation	glgP, glk, malQ, pgm	9.0E−02
Pyrimidine nucleotide de novo biosynthesis	carA, ndk, nrdA, pyrB, pyrC, pyrD, thyX, tmk	8.0E−02
S-Adenosyl-l-methionine biosynthesis	lysC, metA, metB, thrA, PMN2A_1269, PMN2A_1748	7.0E−02
Depleted only in coculture
Aerobic respiration	ctaC, ctaD, ctaE, ndhE, ndhI	9.0E−02
Amine/polyamine/urea degradation	ureA, ureB, ureC	5.0E−02
Carbohydrate biosynthesis	cbbA, gap3, gapA, glgC, malQ, pgk, pgm, rbcL, rbcS, tktA	5.0E−02
Degradation/utilization/assimilation	carA, cbbA, gcvP, gapA, glmU, glnA, malQ, met3, pgk, pgm, rbcL, rbcS, speA, tktA, ureA, ureB, ureC	8.0E−02
Glycolysis	cbbA, eno, gap3, pgk	6.0E−02
Pentose phosphate pathway	gnd, pgl, tktA, zwf	2.0E−02
Pyrimidine nucleobase salvage II	codA, upp	3.0E−02
Superpathway of serine and glycine biosynthesis I	glyA, serA	9.0E−02

^aProchlorococcus metabolic pathways with transcripts that were consistently depleted during the first 5 h of extended darkness (36- and 40-h time points) relative to the controls grown on a 13:11 diel light:dark cycle. Additional details on these and other significantly depleted transcripts can be found in Table S3 in the supplemental material.

^bPathway definitions are from BioCyc (75).

^cP value indicates the result of a Fisher significance test (PathwayTools).