Analysis of microbial gene transcripts in environmental samples.
We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which approximately 80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly alpha- and gamma-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.
Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA.
Rachel S
RS
Poretsky
Nasreen
N
Bano
Alison
A
Buchan
Gary
G
LeCleir
Jutta
J
Kleikemper
Maria
M
Pickering
Whitney M
WM
Pate
Mary Ann
MA
Moran
James T
JT
Hollibaugh
D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D005618:Fresh Water / Q000382:microbiology*; D015723:Gene Library; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D010933:Plankton / Q000235:genetics / Q000378:metabolism; D019642:RNA, Archaeal / Q000032:analysis / Q000235:genetics; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics* / Q000378:metabolism; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012333:RNA, Messenger