Analysis of Microbial Gene Transcripts in Environmental Samples

Poretsky, Rachel; Bano, Nasreen; Buchan, Alison; LeCleir, Gary R.; Kleikemper, Jutta; Pickering, Maria; Pate, Whitney M.; Moran, Mary Ann; Hollibaugh, James T.

doi:10.1128/aem.71.7.4121-4126.2005

Cited by 210 publications

(148 citation statements)

References 17 publications

(14 reference statements)

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“…The function of transposases in open ocean cyanobacteria is unknown, however in other related diazotrophic cyanobacteria, tranposases are present in high genome copy number and recently have been observed as dominant transcripts in situ (Hewson et al, 2009). The large number of conserved hypothetical proteins or proteins of unknown function (31 in the day and eight at night) is consistent with observations in other metatranscriptomic surveys (Poretsky et al, 2005(Poretsky et al, , 2009bFrias-Lopez et al, 2008;Gilbert et al, 2008;McGrath et al, 2008), and shows a need for prioritized studies of gene function.…”

Section: Transcript Library Gene Orthologssupporting

confidence: 64%

“…Unlike metagenomic surveys which elucidate potential genetic capabilities (Tyson et al, 2004;Venter et al, 2004;Rusch et al, 2007), and which are mostly focused on the discovery of novel metabolic pathways or extent of diversity, metatranscriptomics provide information on active processes in dominant microorganisms (Poretsky et al, 2005(Poretsky et al, , 2009bFrias-Lopez et al, 2008). Metatranscriptomic studies to date have elucidated that a large proportion of genes expressed in open ocean assemblages have no known function, or show less similarity to cultivated microorganisms than metagenomic surveys (Frias-Lopez et al, 2008;Gilbert et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Recent application of whole-genome random transcript sequencing (metatranscriptomics) has shown utility for understanding coastal and open ocean microbial community ecophysiology (Poretsky et al, 2005(Poretsky et al, , 2009bFrias-Lopez et al, 2008;Gilbert et al, 2008;Hewson et al, 2009). Unlike metagenomic surveys which elucidate potential genetic capabilities (Tyson et al, 2004;Venter et al, 2004;Rusch et al, 2007), and which are mostly focused on the discovery of novel metabolic pathways or extent of diversity, metatranscriptomics provide information on active processes in dominant microorganisms (Poretsky et al, 2005(Poretsky et al, , 2009bFrias-Lopez et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

et al. 2009

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Trichodesmium are responsible for a large fraction of open ocean nitrogen fixation, and are often found in complex consortia of other microorganisms, including viruses, prokaryotes, microbial eukaryotes and metazoa. We applied a community gene expression (metatranscriptomic) approach to study the patterns of microbial gene utilization within colonies of Trichodesmium collected during a bloom in the Southwest Pacific Ocean in April 2007. The survey generated 5711-day and 5385-night putative mRNA reads. The majority of mRNAs were from the co-occurring microorganisms and not Trichodesmium, including other cyanobacteria, heterotrophic bacteria, eukaryotes and phage. Most transcripts did not share homology with proteins from cultivated microorganisms, but were similar to shotgun sequences and unannotated proteins from open ocean metagenomic surveys. Trichodesmium transcripts were mostly expressed photosynthesis, N 2 fixation and S-metabolism genes, whereas those in the co-occurring microorganisms were mostly involved in genetic information storage and processing. Detection of Trichodesmium genes involved in P uptake and As detoxification suggest that local enrichment of N through N 2 fixation may lead to a P-stress response. Although containing similar dominant transcripts to open ocean metatranscriptomes, the overall pattern of gene expression in Trichodesmium colonies was distinct from free-living pelagic assemblages. The identifiable genes expressed by Trichodesmium and closely associated microorganisms reflect the constraints of life in well-lit and nutrient-poor waters, with biosynthetic investment in nutrient acquisition and cell maintenance, which is in contrast to gene transcription by soil and coastal seawater microbial assemblages. The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies. The ISME Journal (

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Section: Transcript Library Gene Orthologssupporting

confidence: 64%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

et al. 2009

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“…Metatranscriptomics, the sequencing of messenger RNA (mRNA, representing expressed genes) from the environment, provides an unbiased view of the functionality of a microbial community as it is not constrained to targeting a specific phylogenetic group or metabolic pathway (Poretsky et al, 2005). To this point, metatranscriptomic analyses have shown community expression patterns over diel cycles or under enhanced CO 2 concentrations, as well as identified taxon-specific metabolic processes (Frias-Lopez et al, 2008;Gilbert et al, 2008;Hewson et al, 2009;Poretsky et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

et al. 2010

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Dimethylsulfoniopropionate (DMSP) is an important source of reduced sulfur and carbon for marine microbial communities, as well as the precursor of the climate-active gas dimethylsulfide (DMS). In this study, we used metatranscriptomic sequencing to analyze gene expression profiles of a bacterial assemblage from surface waters at the Bermuda Atlantic Time-series Study (BATS) station with and without a short-term enrichment of DMSP (25 nM for 30 min). An average of 303 143 reads were obtained per treatment using 454 pyrosequencing technology, of which 51% were potential protein-encoding sequences. Transcripts from Gammaproteobacteria and Bacteroidetes increased in relative abundance on DMSP addition, yet there was little change in the contribution of two bacterioplankton groups whose cultured members harbor known DMSP degradation genes, Roseobacter and SAR11. The DMSP addition led to an enrichment of transcripts supporting heterotrophic activity, and a depletion of those encoding light-related energy generation. Genes for the degradation of C3 compounds were significantly overrepresented after DMSP addition, likely reflecting the metabolism of the C3 component of DMSP. Mapping these transcripts to known biochemical pathways indicated that both acetyl-CoA and succinyl-CoA may be common entry points of this moiety into the tricarboxylic acid cycle. In a short time frame (30 min) in the extremely oligotrophic Sargasso Sea, different gene expression patterns suggest the use of DMSP by a diversity of marine bacterioplankton as both carbon and sulfur sources.

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“…Recent applications of metatranscriptomics revealed differences in community gene expression in response to tidal and diel cycles (Frias-Lopez et al, 2008;Poretsky et al, 2005;Poretsky et al, in press) and in response to elevated CO 2 concentrations (Gilbert et al, 2008). These studies revealed a large component of sequences that are of unknown origin (that is, no hits to gene databases), including possibly intergenic spacer-encoded riboswitches and termination factors (Frias-Lopez et al, 2008;Gilbert et al, 2008;Poretsky et al, 2005;Poretsky et al, in press). Because sequencing is random, most sequences obtained in metagenomic and metatranscriptomic studies are from abundant taxa, and rarer organisms, such as C. watsonii, may be absent altogether (Johnston et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

et al. 2009

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The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N 2 fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.

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Analysis of Microbial Gene Transcripts in Environmental Samples

Cited by 210 publications

References 17 publications

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

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