Comparative day/night metatranscriptomic analysis of microbial ...

1370 R. S. Poretsky et al.
Table 3. Selected biogeochemically relevant genes in the HOT metatranscriptome.
ecosystem. Compounds such as methanol and formaldehyde
(Heikes et al., 2002; Carpenter et al., 2004; Giovannoni
et al., 2008), methane (Ward et al., 1987), and
methylhalides (Woodall et al., 2001; Schaefer et al., 2002)
may be available to heterotrophic bacterioplankton in
surface sea water. Dimethylsulphoniopropionate, an
organic sulphur compound produced in abundance by
marine phytoplankton (Kiene et al., 2000), is a rich source
of methyl groups for surface ocean bacterioplankton, and
tetrahydrofolate-mediated C1 transfer (i.e. transcripts
mapping to the C1 pool by folate and methane metabolism
KEGG pathway; Table S5) has been shown to play a role
in its metabolism (Howard et al., 2006). Recovery of nearly
Night Day
Nitrogen Nitrogenase (N fixation) nifH, nifU, nifS, nifB + +
Ammonium transport amt + +*
Ammonia monooxygenase amoA
Assimilatory nitrate reductase narB +
Hydroxylamine oxidoreductase hao
Nitrate permease napA +
Nitrite reductase nirA +
Dissimilatory nitrite reductase nirK, nirS
Nitric oxide reductase norQ +
Nitrate transporter narK +
Urease ureC, ureE, ureF + +
Methylotrophy Serine-glyoxylate aminotransferase + +
Formate dehydrogenase fdh, fdsD + +
Methylene tetrahydrofolate reductase metF + +
Methane monooxygenase mmo
Methanol dehydrogenase mxa +
Methenyltetrahydromethanopterin cyclohydrolase mch + +
Crotonyl-CoA reductase + +
Formaldehyde-activating enzyme fae +
Polyamine degradation Deoxyhypusine synthase dys2 +* +
Spermidine/putrescine transport system permease potC +* +
Acetylpolyamine aminohydrolase aphA
Sulphur cycle Sulphur oxidation soxB, soxC, soxA, soxZ, soxF + +
Dimethylsulphoniopropionate demethylase dmdA
Glycine betaine Dimethylglycine dehydrogenase dmgdh + +
Glycine cleavage system (amnomethyltransferase) gcvT +* +
Aromatic compounds Aromatic ring hydroxylase chlP + +*
protocatechuate 3,4-dioxygenase pcaH
Benzoyl-CoA oxygenase boxA +
Carbon monoxide Carbon monoxide dehydrogenase cosS, coxM, coxL + +
Phototrophy and C fixation Photosystem I multiple + +*
Photosystem II multiple + +*
Rubisco rbcL, rbcS + +*
Photosynthetic reaction centre, M subunit pufM +
Proteorhodopsin + +*
Phosphate assimilation Phosphonate uptake phnD, phnC + +
Alkaline phosphatase phoA + +
Phosphate uptake pstA, pstS + +
Amino acid metabolism Glutamate synthase gltB + +
Glutathione reductase gor +* +
Histidine kinase baeS +* +
Threonine synthase thrC +* +
Trace metal uptake Selenium +* +
Iron tonB + +
Arsenite +
Arsenate reductase arsC + +
A‘+’ indicates occurrence in the night or day sample. An asterisk indicates significantly higher transcript frequency in one.
four times as much mRNA per volume of sea water in the
day (~30 ng l -1 ) compared with night (~8 ngl -1 ) is consistent
with high relative abundance of RNA polymerase
transcripts in the day (Table 2) and likely reflects increased
gene expression when solar radiation is available.
Night-biased synthesis of vitamin B6, essential for a
variety of amino acid conversions including transaminations,
decarboxylations and dehydrations, in conjunction
with evidence for other night-time activities such as the
g-glutamyl pathway for amino acid uptake, the overrepresentation
of amino acid transport and metabolism genes,
and the histidine synthesis pathway (Table 3 and
Tables S4–S6), indicate that amino acid acquisition in
© 2009 The Authors
Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 11, 1358–1375