Evidence for a clade‐specific temporal and spatial separation in ribulose bisphosphate carboxylase gene expression in phytoplankton populations off Cape Hatteras and Bermuda

Paul, John H.; Pichard, Scott L.; Kang, Jordan B.; Watson, G. M.; Tabita, F. Robert

doi:10.4319/lo.1999.44.1.0012

Cited by 31 publications

(43 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Results of diel sampling from this study (Figure 4b and Supplementary data) and from our and others' previous work (Pichard et al, 1996;Paul et al, 1999Paul et al, , 2000bWyman, 1999) demonstrate that much of the cellular RuBisCO RNA pools fluctuate daily, with peak concentrations tending toward early morning hours. Diel variability here was most pronounced for the heterokont group rbcL RNA (Figure 4b), with the minimum concentration only about 10% of the maximum (other rbcL clades' diel results shown in Supplementary data).…”

Section: Phytoplankton Cell Numbersmentioning

confidence: 99%

Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume

et al. 2007

View full text Add to dashboard Cite

River plumes deliver large quantities of nutrients to oligotrophic oceans, often resulting in significant CO 2 drawdown. To determine the relationship between expression of the major gene in carbon fixation (large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, RuBisCO) and CO 2 dynamics, we evaluated rbcL mRNA abundance using novel quantitative PCR assays, phytoplankton cell analyses, photophysiological parameters, and pCO 2 in and around the Mississippi River plume (MRP) in the Gulf of Mexico. Lower salinity (30-32) stations were dominated by rbcL mRNA concentrations from heterokonts, such as diatoms and pelagophytes, which were at least an order of magnitude greater than haptophytes, a-Synechococcus or high-light Prochlorococcus. However, rbcL transcript abundances were similar among these groups at oligotrophic stations (salinity 34-36). Diatom cell counts and heterokont rbcL RNA showed a strong negative correlation to seawater pCO 2 . While Prochlorococcus cells did not exhibit a large difference between low and high pCO 2 water, Prochlorococcus rbcL RNA concentrations had a strong positive correlation to pCO 2 , suggesting a very low level of RuBisCO RNA transcription among Prochlorococcus in the plume waters, possibly due to their relatively poor carbon concentrating mechanisms (CCMs). These results provide molecular evidence that diatom/pelagophyte productivity is largely responsible for the large CO 2 drawdown occurring in the MRP, based on the cooccurrence of elevated RuBisCO gene transcript concentrations from this group and reduced seawater pCO 2 levels. This may partly be due to efficient CCMs that enable heterokont eukaryotes such as diatoms to continue fixing CO 2 in the face of strong CO 2 drawdown. Our work represents the first attempt to relate in situ microbial gene expression to contemporaneous CO 2 flux measurements in the ocean.

show abstract

Section: Phytoplankton Cell Numbersmentioning

confidence: 99%

Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume

et al. 2007

View full text Add to dashboard Cite

show abstract

“…rbcL mRNA analysis. mRNA was extracted from seawater using RNeasy spin columns (Qiagen) as described elsewhere (Paul 2001). Briefly, between 200 and 800 ml seawater samples were treated with 0.1% v/v DEPC (diethyl-pyrocarbonate; Sigma Chemical) and filtered onto 25 mm, 0.45 µm HV polyvinylidene difluoride filters (Millipore Durapore).…”

Section: Methodsmentioning

confidence: 99%

“…RNA was then immobilized onto Zeta-Probe charged nylon filters (Bio-Rad) by dot-blotting and UV-crosslinking. Duplicate samples were probed with form IA, form IB and form ID rbcL probes as previously described (Watson & Tabita 1996, Paul et al 1999. Riboprobes labeled with 35 S-UTP (uridine triphosphate) were prepared by in vitro transcription.…”

Section: Methodsmentioning

confidence: 99%

High rates of ammonium recycling drive phytoplankton productivity in the offshore Mississippi River plume

Wawrik¹,

Paul²,

Bronk³

et al. 2004

Aquat. Microb. Ecol.

View full text Add to dashboard Cite

As part of an integrated study of the regulation of carbon fixation in the offshore Mississippi River plume, we measured the rates of 15 N-labeled ammonium and nitrate uptake in the surface plume waters from offshore to nearshore along the plume axis towards the Mississippi Delta. Concentrations of nitrate in the plume ranged from 0.19 to 2.5 µM with the highest concentrations primarily in the shoreward stations, while ammonium ranged from 0.17 to 0.44 µM, showing little spatial variability. Rates of ammonium uptake ranged from 16.5 to 260 nM h -1 , and showed a strong trend of increasing values from offshore towards the Mississippi Delta. In contrast, nitrate uptake rates ranged from 3.2 to 25 nM h -1 . The high rates of ammonium uptake in the presence of low ammonium concentrations and elevated nitrate was made possible by elevated rates of ammonium regeneration that exceeded ammonium uptake by 1.7 to 5.7-fold in the plume. The plume exhibited relatively low f-ratios and also contained elevated levels of Synechococcus as determined by flow cytometry and high levels of form IA (α-cyanobacterial) rbcL transcripts. These data suggest that a major portion of the carbon fixation observed in the offshore Mississippi River plume represents recycled production supported by high rates of ammonium regeneration.KEY WORDS: Gulf of Mexico · Mississippi River plume · Nitrate uptake · Ammonium uptake · Nutrient cycling Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 35: [175][176][177][178][179][180][181][182][183][184] 2004 No targeted survey of the plume in this environment has thus far been conducted to study the plume's effect on oligotrophic ocean ecology, phytoplankton composition and nutrient cycling. Previous studies of the plume have primarily been concerned with the plume's impact on coastal ecosystems in the northern GOM shelf region. The plume has, however, been shown to greatly enhance oligotrophic surface productivity and phytoplankton species composition in the oligotrophic GOM (Wawrik et al. 2003).On the shelf, nutrients, irradiance and primary production of the Mississippi River plume have been studied extensively (Lohrenz et al. 1990, Dortch & Whitledge 1992, Pakulski et al. 1995, 2000. Productivity in the most coastal region of the plume is initially limited by turbidity, and highest productivity occurs at intermediate salinities as the plume matures. Nutrients display distinct non-conservative mixing behavior along the salinity gradient of the plume, and both silicate as well as nitrogen have been reported to limit productivity in the higher salinity portions of the plume. High productivity in the plume has been implicated in the formation of extensive regions of hypoxia in bottom waters along the Louisiana and Texas shelf during summer stratification (Dortch et al. 1994, Eadie et al. 1994, Justic et al. 1996.Nitrogen mineralization rates in the Mississippi River plume area have been measured using High Performance Liquid Chromatography (HPLC...

show abstract

“…Each filter was then hybridized with a probe derived from Cylindrotheca sp. strain N1 (23). A 35 S-labeled riboprobe was generated by in vitro transcription of linearized plasmid DNA with 35 S-UTP.…”

Section: Methodsmentioning

confidence: 99%

Real-Time PCR Quantification of rbcL (Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase) mRNA in Diatoms and Pelagophytes

Wawrik

Paul

Tabita

2002

Appl Environ Microbiol

114

View full text Add to dashboard Cite

Transcriptional activity is often used as a surrogate for gene expression in environmental microbial communities. We developed a real-time PCR assay in which the ABI-Prism (PE Applied Biosystems) detection system is used for quantification of large-subunit ribulose-1,5-bisphosphate caboxylase/oxygenase (rbcL) mRNA in diatoms and pelagophytes both in cultures and from natural phytoplankton communities. Plasmid DNA containing rbcL inserts, as well as in vitro transcribed mRNA of the plasmids, was used to generate standard curves with a dynamic range of more than 6 orders of magnitude with high accuracy and precision (R 2 ‫؍‬ 0.998). Expression levels in a cultured diatom (Phaeodactylum tricornutum) were quantified through one light-dark cycle by using traditional 35 S-labeled oligonucleotide hybridization and real-time PCR. The mRNA levels detected by the two techniques were similar and correlated well (R 2 ‫؍‬ 0.95; slope ‫؍‬ 1.2). The quantities obtained by hybridization were slightly, yet significantly, larger (t ‫؍‬ 5.29; P ‫؍‬ 0.0011) than the quantities obtained by real-time PCR. This was most likely because partially degraded transcripts were not detected by real-time PCR. rbcL mRNA detection by real-time PCR was 3 orders of magnitude more sensitive than rbcL mRNA detection by hybridization. Diatom and pelagophyte rbcL mRNAs were also quantified in a profile from an oligotrophic site in the Gulf of Mexico. We detected the smallest amount of diatom rbcL expression in the surface water and maximum expression at a depth that coincided with the depth of the subsurface chlorophyll maximum. These results indicate that real-time PCR may be utilized for quantification of microbial gene expression in the environment.One of the continuing challenges in microbial ecology is to estimate microbial activity. Even small water or soil samples usually contain large numbers of diverse microbial species, yet it is difficult to determine the individual contributions of the species to particular processes by using bulk assay techniques. While tremendous advances have been made since quantitative methods for analysis of nucleic acids via various hybridization techniques (27, 28, 34) became available, applications have generally been limited by the sensitivity of the procedures. Such methods for quantification of gene expression have traditionally involved the use of radiolabeled probes for detection of a particular mRNA cross-linked to charged filters. These protocols are time-consuming and costly and involve generation of radioactive waste. PCR technology has greatly increased the sensitivity of methods for gene detection, but it is inherently nonquantitative. Quantitative PCR combines the sensitivity of PCR with real-time measurement of amplification and thus allows quantification of the original target concentration.A PCR-based quantitative assay, first described by Holland et al. (13) and referred to as a real-time PCR, has recently emerged (6, 11). While this technique offers all the advantages of conventional PCR, such as ...

show abstract

Evidence for a clade‐specific temporal and spatial separation in ribulose bisphosphate carboxylase gene expression in phytoplankton populations off Cape Hatteras and Bermuda

Cited by 31 publications

References 58 publications

Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume

Phytoplankton carbon fixation gene (RuBisCO) transcripts and air-sea CO2 flux in the Mississippi River plume

High rates of ammonium recycling drive phytoplankton productivity in the offshore Mississippi River plume

Real-Time PCR Quantification of rbcL (Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase) mRNA in Diatoms and Pelagophytes

Contact Info

Product

Resources

About