Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.
Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with marine DOM cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight DOM (HMWDOM) addition. The cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over time. In contrast, the DOM-amended microcosm doubled in cell numbers over 27 h, and a variety of HMWDOM-stimulated transcripts from different taxa were observed at all time points measured relative to the control. Transcripts significantly enriched in the HMWDOM treatment included those associated with two-component sensor systems, phosphate and nitrogen assimilation, chemotaxis, and motility. Transcripts from Idiomarina and Alteromonas spp., the most highly represented taxa at the early time points, included those encoding TonB-associated transporters, nitrogen assimilation genes, fatty acid catabolism genes, and TCA cycle enzymes. At the final time point, Methylophaga rRNA and non-rRNA transcripts dominated the HMWDOM-amended microcosm, and included gene transcripts associated with both assimilatory and dissimilatory single-carbon compound utilization. The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover. These findings suggest that coordinated, cooperative activities of a variety of bacterial "specialists" may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
McCarren
Jay
J
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Becker
Jamie W
JW
Repeta
Daniel J
DJ
Shi
Yanmei
Y
Young
Curtis R
CR
Malmstrom
Rex R
RR
Chisholm
Sallie W
SW
DeLong
Edward F
EF
D002244:Carbon / Q000378:metabolism; D030541:Databases, Genetic; D017753:Ecosystem; D020869:Gene Expression Profiling; D053858:Metabolic Networks and Pathways; D056186:Metagenomics; D008827:Microbiological Phenomena; D008954:Models, Biological; D008969:Molecular Sequence Data; D009930:Organic Chemicals / Q000378:metabolism; D012623:Seawater / Q000737:chemistry* / Q000382:microbiology*; D014871:Water Microbiology
D009930:Organic Chemicals; D002244:Carbon
FEMS Microbiol Ecol. 2001 Jan;34(3):243-253
11137604
PLoS Biol. 2007 Mar;5(3):e16
17355171
ISME J. 2007 Oct;1(6):480-91
18043650
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
16820507
Nucleic Acids Res. 2007;35(21):7188-96
17947321
Appl Environ Microbiol. 2003 Jan;69(1):199-211
12513996
Bioinformatics. 2007 Jan 1;23(1):127-8
17050570
Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14674-9
11121068
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
18077471
Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5
19004872
Environ Microbiol. 2008 Jun;10(6):1526-35
18294205
Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18036-41
15596722
Science. 2005 Aug 19;309(5738):1242-5
16109880
ISME J. 2008 Dec;2(12):1194-212
18670397
Environ Microbiol. 2010 Jan;12(1):118-23
19725865
Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
14985472
Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8
20363958
PLoS One. 2008 Aug 22;3(8):e3042
18725995
Science. 1992 Mar 20;255(5051):1561-4
17820170
Science. 2001 May 4;292(5518):917-20
11340202
ISME J. 2010 Nov;4(11):1410-20
20463763
Appl Environ Microbiol. 2007 Aug;73(16):5261-7
17586664
Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10
18316740
Int J Syst Evol Microbiol. 2004 Sep;54(Pt 5):1773-1788
15388743
Environ Microbiol. 2006 Nov;8(11):2022-30
17014500
Appl Environ Microbiol. 1997 Jan;63(1):186-93
16535483
Appl Environ Microbiol. 2004 Nov;70(11):6753-66
15528542
Bioinformatics. 2010 Jan 1;26(1):136-8
19855105
Nat Methods. 2009 Sep;6(9):639-41
19668203
ISME J. 2010 Jul;4(7):896-907
20220791
Nature. 2008 Apr 10;452(7188):741-4
18337719
Appl Environ Microbiol. 2008 Dec;74(23):7321-8
18849453
Environ Microbiol. 2007 Oct;9(10):2417-29
17803768
Nature. 2009 May 14;459(7244):266-9
19444216
Bioinformatics. 2009 Oct 15;25(20):2737-8
19696045