Comparative day/night metatranscriptomic analysis of microbial ...

Depth (m)
0
50
100
150
200
sequences, Proteobacteria were most abundant (41%;
Fig. 3) and were dominated by a-Proteobacteria (22%),
b-Proteobacteria (8%) and g-Proteobacteria (8%).
Bacteroidetes (8%) and Firmicutes (12%, biased towards
the day sample) were also well represented.
Taxonomically binned mRNA sequences were compared
with community composition data to ask whether
taxa contributed to the HOT community mRNA in proportion
to their representation in the microbial assemblage
(i.e. whether taxa are equally transcriptionally active on a
per-cell basis). Cyanobacteria dominated the transcript
libraries (55% of sequences) with about twofold higher
representation than in the 16S rRNA amplicons or the cell
count data (Fig. 3), indicating that there is more gene
expression in these autotrophic bacterioplankton than in
co-occurring heterotrophs (or possibly that their transcripts
are longer-lived). When relative 16S rRNA abundance
was calculated among just the heterotrophic
groups (i.e. with cyanobacterial sequences removed),
many taxa had similar contributions to the transcript pool
and amplicon pool, suggesting comparable levels of
transcriptional activity on a per-gene basis within the limits
of recognized biases of PCR amplification (Fig. 3).
0 200 400 600
chla (10 -3 μg l -1 )
Prochlorococcus x 10 3 cells ml -1
Synechococcus x 10 2 cells ml -1
Nanoeukaryotes x 10 2 cells ml -1
Heterotrophic bateria x 10 3 cells ml -1
Comparative Metatranscriptomic Analysis 1361
Fig. 2. Depth profiles of Prochlorococcus-like, Synechococcus-like, heterotrophic bacteria and pigmented nanoeukaryotes during the HOT-175
cruise, as determined by flow cytometry. The horizontal line indicates the mixed layer depth. The depth profile for chlorophyll a is also
indicated. Data were collected through the HOT project and downloaded from the HOT Data Organization and Graphical System
(http://hahana.soest.hawaii.edu/hot/hot-dogs/).
Proteobacteria contributed the second largest number of
transcript sequences (28%), most of which were attributed
to a-Proteobacteria (19%) and g-Proteobacteria
(4%). Approximately 2% of the total transcripts were of
eukaryotic origin. Comparing putative taxonomic assignments
of transcripts between day and night, Cyanobacteria
contributed equally to the day and night transcriptome
(55% versus 56%) as did a-Proteobacteria (40% versus
45% of heterotrophic transcripts) and g-Proteobacteria
(11% versus 8% of heterotrophic transcripts) (Fig. 3).
More detailed taxonomic assignment of transcripts was
carried out for the best represented clades. The Cyanobacteria
transcripts were dominated by Prochlorococcuslike
sequences most similar to P. marinus AS9601,
P. marinus MIT 9301 and P. marinus MIT 9312 (Table 1).
The a-Proteobacteria, the most transcriptionally active
among the heterotrophic groups, mostly contained
sequences with similarity to the SAR11 group members
P. ubique HTCC1002 and P. ubique HTCC1062 (~10% of
prokaryotic transcripts). Roseobacter-like sequences
were also represented and were primarily assigned to
Dinoroseobacter shibae DFL 12, Jannaschia sp. CCS1,
Silicibacter pomeroyi DSS-3, Roseobacter denitrificans
© 2009 The Authors
Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 11, 1358–1375