Incorporation versus biosynthesis of leucine: implications for measuring rates of protein synthesis and biomass production by bacteria in marine systems

Kirchman, DL; Sy, Newell; Hodson, RE

doi:10.3354/meps032047

Cited by 100 publications

(71 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…fatty acids Dark bicarbonate assimilation by Arctic bacteria L Alonso-Sáez et al biosynthesis and anaplerotic reactions, do not lead to any net C assimilation. Leucine-to-carbon conversion factors are also largely unconstrained due to processes such as intracellular protein turnover or leucine catabolism, which has been shown to intensify under oligotrophic conditions (Kirchman et al, 1986, Alonso-Sáez et al, 2007. In general, the metabolic changes undergone by cells during the stationary phase have been poorly characterized, but our results suggest that the incorporation of CO 2 could be of great importance for the metabolism of such resources-depleted bacteria.…”

Section: Discussionmentioning

confidence: 49%

High bicarbonate assimilation in the dark by Arctic bacteria

et al. 2010

View full text Add to dashboard Cite

Although both autotrophic and heterotrophic microorganisms incorporate CO 2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5-2.5 lg C L À1 d À1 ) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO 2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40-70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta-and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO 2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.

show abstract

Section: Discussionmentioning

confidence: 49%

High bicarbonate assimilation in the dark by Arctic bacteria

et al. 2010

View full text Add to dashboard Cite

show abstract

“…suspended particular organic carbon (SuspPOC), sediment particular organic carbon (SedPOC), and dissolved organic carbon (DOC), were taken from the studies of Asmus & Asmus (1993, 1998) and R. . Data on the biomass of sediment and pelagic bacteria were obtained from Kirchman et al (1986), Schulz (1990) and Rusch et al (2001). The biomass, rates of gross primary (GPP) and net primary (NPP) production of the 3 primary producer communities, namely phytoplankton, microphytobenthos and macrophytes were given by Asmus & Bauerfeind (1994) and R. .…”

Section: Methodsmentioning

confidence: 99%

Energy flow of a boreal intertidal ecosystem, the Sylt-Rømø Bight

Baird¹,

Asmus

Asmus³

2004

Mar. Ecol. Prog. Ser.

View full text Add to dashboard Cite

A detailed energy flow model consisting of 56 living and 3 non-living compartments was assembled for the intertidal area of the Sylt-Rømø Bight. The model depicts the biomass of each compartment, carbon flow between the components, imports and exports, as well as an energy budget for each. The food web was analysed by means of network analysis which showed that about 17% of the total daily flow through the system is recycled through a complex cycling structure consisting of 1197 cycles. The cycling network indicated that about 99% of the recycling involves 2 to 3 compartments, with sediment bacteria and particulate organic carbon (POC) participating in most instances. Input/output analyses indicated that phytoplankton production in the Bight does not satisfy the demands of filter-feeders on an annual average basis so that about 160 mg C m -2 d -1 of phytoplankton have to be imported. We compared several dimensionless system level indices, such as internalised and normalised A/DC (ascendancy/development capacity) ratios, calculated for the Bight with those of other marine and estuarine ecosystems on a global basis. These comparisons showed that energy is rather inefficiently transferred within the Bight at a mean trophic efficiency index of 2.61%, and that most of the system level indices are lower than those of other coastal ecosystems. However, higher values were obtained for flow diversity and food web connectance compared to other systems. This study has revealed the Bight to be a highly complex system whose energy pathways appear to be sensitive to external perturbations.

show abstract

“…Bacteria and cyanobacteria were enumerated using a A 0 direct count method outlined in Turley & Hughes (1992). 3H-thymidine (Fuhrman & Azam 1980, 1982, JGOFS 1990) and 3H-leucine (Kirchman et al 1985(Kirchman et al , 1986) incorporation rates were determined by adding 5 nM (final concentration) to five 10 to 40 m1 replicates (2 of which were glutaraldehyde treated controls) of seawater from each depth and incubating for 1 to 4 h at in situ temperatures. Sample size and incubation duration increased with depth.…”

Section: Methodsmentioning

confidence: 99%

Biogeochemical significance of attached and free-living bacteria and the flux of particles in the NE Atlantic Ocean

Turley¹,

Mackie²

1994

Mar. Ecol. Prog. Ser.

118

102

View full text Add to dashboard Cite

In the NE Atlantic during May 1990, a period of high aggregate abundance, amorphous aggregates contained substantially higher concentrations of bacteria, cyanobacteria and flagellates than the surrounding seawater. Those from 45 to 55 m, at the aggregate maximum just below the seasonal thermocline, contained 2.1 to 25.4 X 10' bacteria, 1.0 to 4.7 X 10' cyanobacteria and 1.3 to 33.0 X 106 flagellates ml-' aggregate. Leucine incorporation rates by bacteria attached to aggregates ranged from 12 to 206 X 10-*' m01 cell-' d-' The concentration of bacteria associated with faecal pellets was generally higher than the concentration on the amorphous aggregates. Bacteria attached to aggregates were equivalent to 10 and 14 % of free-living bacterial carbon integrated through the water column to 100 and 300 m, respectively. This could rise to 25 and 34% if the different carbon content of attached and free-living bacteria was taken into account. However, this study coincided with the maximum marine snow concentration measured 150 km southwest, so at other times when marine snow concentrations are lower, the proportion of attached bacteria will be less. The contribution of attached bacteria to total bacterial production in the top 100 and 300 m ranges between 1.8 and 3.4 %. The contribution of free-living bacterial carbon to suspended POC (particulate organic carbon) was between 25 and 33% and after correcting for their retention on the glass fibre filters, this contribution could be 28 to 40%. Flux studies during 1989 and 1990 indicated that a smaller proportion of POC flux (9 %) and bacterial carbon flux (10%) reached 3100 m than mass flux (25 and 35%), indicating there are processes involved which preferentially utilise or reduce the POC and bacterial components. Bacterial detachment from sinking particles could contribute 2.4 % of the integrated bacterial biomass per annum. The fraction of sink~ng POC lost between 150 and 3100 m may be an important carbon source to the mid/deep-water bacterial population, capable of supplying around 90% of the bacterial carbon demand during April to July 1989 at 47" N, 20°W. In the deeper waters, between 600 and 3100 m, there was sufficient depth-dissipated sinking POC to potentially supply the carbon demand of the bacteria. However, above 600 m an additional source of organic carbon is required to support their growth.

show abstract

Incorporation versus biosynthesis of leucine: implications for measuring rates of protein synthesis and biomass production by bacteria in marine systems

Cited by 100 publications

References 14 publications

High bicarbonate assimilation in the dark by Arctic bacteria

High bicarbonate assimilation in the dark by Arctic bacteria

Energy flow of a boreal intertidal ecosystem, the Sylt-Rømø Bight

Biogeochemical significance of attached and free-living bacteria and the flux of particles in the NE Atlantic Ocean

Contact Info

Product

Resources

About