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Abstract:
Bulk mRNA was used to explore the transcriptional
activity of bacterial communities in oxic versus
anoxic paddy soil. Two microbial cDNA libraries were
constructed from composite samples using semirandomly
primed RT-PCR. cDNAs averaged 500–
600 bp in length and were treated as expressed
sequence tags (ESTs). Clustering analysis of 805
random cDNAs resulted in 179 and 155 different ESTs
for the oxic and anoxic zones respectively. Using an
E-value threshold of e-10, a total of 218 different ESTs
could be assigned by BLASTX, while 116 ESTs were
predicted novel. Both the proportion and significance
of the EST assignments increased with cDNA length.
Taxonomic assignment was more powerful in discriminating
between the aerobic and anaerobic bacterial
communities than functional inference, as most
ESTs in both oxygen zones were putative indicators
of similar housekeeping functions, in particular ABCtype
transporters. A few ESTs were putative indicators
for community function in a biogeochemical
context, such as b-oxidation of long-chain fatty acids
specifically in the oxic zone. Expressed sequence
tags assigned to Alpha- and Betaproteobacteria were
predominantly found in the oxic zone, while those
affiliated with Deltaproteobacteria were more frequently
detected in the anoxic zone. At the genus
level, multiple assignments to Bradyrhizobium and
Geobacter were unique to the oxic and anoxic zones
respectively. The phylum-level affiliations of 93 16S
rRNA sequences corresponded well with two taxonomically
distinct EST patterns. Expressed sequence
tags affiliated with Acidobacteria and Chloroflexi
were frequently detected in both oxygen zones. In
summary, the soil metatranscriptome is accessible
for global analysis and such studies have great
potential in elucidating the taxonomic and functional
status of soil bacterial communities, but study significance
depends on the number and length of cDNAs
being randomly analysed.
