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Leucine incorporation as a measure of biomass production by heterotrophic bacteria
... Bacterial production was determined onboard using 3 Hleucine incorporation (Kirchman, 2018) and microcentrifugation (Smith and Azam, 1992) as detailed in Van Wambeke et al. (2018). Briefly, triplicate 1.5 ml samples and a control killed with trichloroacetic acid (TCA; 5% final concentration) were incubated with a mixture of [4,5-3 H]-leucine (Perkin-Elmer, specific activity 100 Ci mmol -1 ) and nonradioactive leucine at final concentrations of 14 and 7 nM, respectively. ...
... Along the same lines, Björkman and co-authors found that despite HB and Prochlorococcus being equal competitors for phosphate in the North Pacific, HB is more effective at scavenging ATP (Björkman et al., 2012). In the South Pacific, (Van Wambeke et al. 2008, 2018 found that HB were mainly limited by the availability of energy or labile carbon, as glucose additions stimulated HB production rates to a larger extent than phosphate or nitrogen (Van Wambeke et al. 2008, 2018. ATP molecules contain three atoms of P, five atoms of nitrogen, 10 atoms of carbon and several hydrogen and oxygen atoms. ...
... Along the same lines, Björkman and co-authors found that despite HB and Prochlorococcus being equal competitors for phosphate in the North Pacific, HB is more effective at scavenging ATP (Björkman et al., 2012). In the South Pacific, (Van Wambeke et al. 2008, 2018 found that HB were mainly limited by the availability of energy or labile carbon, as glucose additions stimulated HB production rates to a larger extent than phosphate or nitrogen (Van Wambeke et al. 2008, 2018. ATP molecules contain three atoms of P, five atoms of nitrogen, 10 atoms of carbon and several hydrogen and oxygen atoms. ...
The oceanic dissolved organic phosphorus (DOP) pool is mainly composed of P-esters and, to a lesser extent, equally abundant phosphonate and P-anhydride molecules. In phosphate-limited ocean regions, diazotrophs are thought to rely on DOP compounds as an alternative source of phosphorus (P). While both P-esters and phosphonates effectively promote dinitrogen (N2) fixation, the role of P-anhydrides for diazotrophs is unknown. Here we explore the effect of P-anhydrides on N2 fixation at two stations with contrasting biogeochemical conditions: one located in the Tonga trench volcanic arc region (“volcano,” with low phosphate and high iron concentrations), and the other in the South Pacific Gyre (“gyre,” with moderate phosphate and low iron). We incubated surface seawater with AMP (P-ester), ATP (P-ester and P-anhydride), or 3polyP (P-anhydride) and determined cell-specific N2 fixation rates, nifH gene abundance, and transcription in Crocosphaera and Trichodesmium. Trichodesmium did not respond to any DOP compounds added, suggesting that they were not P-limited at the volcano station and were outcompeted by the low iron conditions at the gyre station. Conversely, Crocosphaera were numerous at both stations and their specific N2 fixation rates were stimulated by AMP at the volcano station and slightly by 3polyP at both stations. Heterotrophic bacteria responded to ATP and 3polyP additions similarly at both stations, despite the contrasting phosphate and iron availability. The use of 3polyP by Crocosphaera and heterotrophic bacteria at both low and moderate phosphate concentrations suggests that this compound, in addition to being a source of P, can be used to acquire energy for which both groups compete. P-anhydrides may thus leverage energy restrictions to diazotrophs in the future stratified and nutrient-impoverished ocean.
... The mean disintegrations per minute (DPM) of the TCA-killed blanks were removed 243 from the mean DPM of the respective samples and succeeding DPM value converted into leucine 244 incorporation rates. PHP was calculated using a conservative theoretical conversion factor of 1.55 245 kg C moL -1 Leu assuming no internal isotope dilution (Kirchman, 1993 Results 270 ...
In the face of climate change there is a need to reduce atmospheric CO 2 concentrations. Artificial upwelling of nutrient-rich deep waters has been proposed as a method to enhance the biological carbon pump in oligotrophic oceanic regions in order to increase carbon sequestration. However, the fate of the newly produced organic matter, and specifically of its resulting dissolved fraction, is not clearly understood. Here we examine the effect of different upwelling intensities and modes (single pulse versus recurring pulses) on the dissolved organic matter pool (DOM). We introduced nutrient-rich deep water to large scale mesocosms (∼44 m ³ ) in the oligotrophic subtropical North Atlantic and found that artificial upwelling strongly increased DOM concentrations and changed its characteristics. The magnitude of the observed changes was related to the upwelling intensity: more intense treatments led to higher accumulation of dissolved organic carbon (>70 μM of excess DOC over ambient waters for the most intense) and to comparatively stronger changes in DOM characteristics (increased proportions of chromophoric DOM (CDOM) and humic-like fluorescent DOM), suggesting a transformation of the DOM pool at the molecular level. Moreover, the single upwelling pulse resulted in higher CDOM quantities with higher molecular weight than the recurring upwelling mode. Together, our results indicate that under artificial upwelling, large DOM pools may accumulate in the surface ocean without being remineralised in the short-term. Possible reasons for this persistence could be a combination of the molecular diversification of DOM due to microbial reworking, nutrient limitation and reduced metabolic capabilities of the prokaryotic communities inside the mesocosms. Our study demonstrates the importance of the DOC pool when assessing the carbon sequestration potential of artificial upwelling.
... The mean disintegrations per minute (DPM) of the TCA-killed blanks were removed from the mean DPM of the respective samples and succeeding DPM value converted into leucine incorporation rates. PHP was calculated using a conservative theoretical conversion factor of 1.55 kg C moL -1 Leu assuming no internal isotope dilution (Kirchman, 1993). The PHP data are available at the PANGAEA repository (Baumann et al., 2021a). ...
In the face of climate change there is a need to reduce atmospheric CO2 concentrations. Artificial upwelling of nutrient-rich deep waters has been proposed as a method to enhance the biological carbon pump in oligotrophic oceanic regions in order to increase carbon sequestration. Here we examine the effect of different artificial upwelling intensities and modes (single pulse versus recurring pulses) on the dynamics of the dissolved organic matter pool (DOM). We introduced nutrient-rich deep water to large scale mesocosms (~44 m³) in the oligotrophic subtropical North Atlantic and found that artificial upwelling strongly increased DOM concentrations and changed its characteristics. The magnitude of the observed changes was related to the upwelling intensity: more intense treatments led to higher accumulation of dissolved organic carbon (>70 μM of excess DOC over ambient waters for the most intense) and to comparatively stronger changes in DOM characteristics (increased proportions of chromophoric DOM (CDOM) and humic-like fluorescent DOM), suggesting a transformation of the DOM pool at the molecular level. Moreover, the single upwelling pulse resulted in higher CDOM quantities with higher molecular weight than the recurring upwelling mode. Together, our results indicate that under artificial upwelling, large DOM pools may accumulate in the surface ocean without being remineralized in the short-term. Possible reasons for this persistence could be a combination of the molecular diversification of DOM due to microbial reworking, nutrient limitation and reduced metabolic capabilities of the prokaryotic communities within the mesocosms. Our study demonstrates the importance of the DOC pool when assessing the carbon sequestration potential of artificial upwelling.
... Generally speaking, PA samples generally showed higher diversity than FL samples [9]. PA bacteria generally have higher enzymatic activity rates [10], higher cell-speci c activity than surrounding bacteria [11,12], and can colonize almost all types of granular organic matter [7], composed of relatively abundant anaerobic bacteria and those taxa preferring low-oxygen conditions [13], thus causing PA bacteria more active than the FL bacteria, playing an important role in nutrient cycling. ...
Cyanobacterial blooms are very common phenomenon in freshwater ecosystems, influencing the composition and function of bacterioplankton communities. However, the drivers on the pattern and mechanism of bacterial community were still little known especially before and after bloom. Here, high-throughput sequencing of bacterial 16S rRNA gene was used to investigate the dynamics of communities with two lifestyles of free-living (FL, 0.22-3 μm) and particle-attached (PA, > 3 μm) in the Lake Taihu, and co-occurrence patterns and assembly mechanism of bacteria were also explored between pre-bloom and post-bloom periods. The results exhibited that the bloom event significantly changed the composition and diversity of plankton community. Primarily, phyla of Proteobacteria, Actinobacteria and Bacteroidetes were dominated in FL bacteria, whereas Proteobacteria, Cyanobacteria and Bacteroidetes were distributed in PA bacteria. Additionally, PA bacteria had higher α-diversity than FL bacteria in two periods. Co-occurrence network analysis revealed that the network was more complex interactions and modularity in the pre-bloom than post-bloom. In addition, multispecies cooperation with negative correlations in the network implied more contribution to the stability and resilience of community in the pre-bloom. Null-model analysis indicated homogeneous selection was the key assembly process in the pre-bloom, while stochastic processes played predominant role in the post-bloom. Moreover, abiotic factors were significantly correlated with keystone taxa to further reveal the deterministic process in the pre-bloom ( p < 0.05). Overall, these findings indicate the ecological network and assembly mechanisms of bacteria driven by environmental factors in the pre-bloom more than post-bloom in a changing aquatic niche.
... To calculate biomass production, the following conversion factors were applied: molecular weight of leucine of 131.2 g/mol, the fraction of leucine per protein of 0.073, the ratio of cellular carbon to the protein of 0.86, and 2.22 Â 10 6 dpm/mCi to convert disintegrations per minute (the measure of radioactivity) to mCi. A factor of 1.55 kg C mol leucine 21 was used to convert the incorporation of leucine to carbon equivalents, assuming no isotope dilution (88). ...
As a window into the past, this study offers insights into the potential role that microbial guilds may have played in the production and recycling of organic matter in ancient Proterozoic ocean chemoclines. The new observations described here suggest that chloroplasts of eukaryotic algae were persistent in the low-oxygen upper chemocline along with the purple and green sulfur bacteria known to dominate the lower half of the chemocline.
... Liquid scintillation cocktail (1.5 ml; Lumagel Safe, Lumac-LSC) was added directly to the microcentrifuge tube, and the activity of the cold TCA insoluble macromolecules was determined using a liquid scintillation counter (LKB, Rack Beta II). Rates of incorporated leucine (pmol leu L -1 h -1 ) were converted to BP (mmol C m -3 d -1 ) using a standard conversion factor (CF = 1.5 kg C mol leucine -1 ; Kirchman, 1993). ...
The effects of benthic dissolved organic carbon (DOC) flux on the dynamics of DOC in the deep continental margins (200 – 2000 m depth) is poorly understood. We investigated heterotrophic prokaryotes (hereafter bacteria) production (BP) and the bio-reactive properties of sediment-derived dissolved organic matter (SDOM) to elucidate microbially mediated cause-effect relationships regarding the rapid consumption of dissolved oxygen (DO) and accumulation of humic-like fluorescent DOM (FDOMH) in the deep-water column (750 – 2000 m depth range) of the Ulleung Basin (UB) in the East Sea. BP in the deep water (2.2 μmol C m⁻³ d⁻¹) of the UB was among the highest reported for various deep-sea sites. The high DOC concentration (55 μM) likely supported the high BP seen in the deep-water column of the UB. Concentrations of DOC and C1 component of the FDOMH, which is indicative of microbial metabolic by-products, were 13-fold and 20-fold greater, respectively, in pore water than in the overlying bottom water, indicating that the sediment in the continental margins is a significant source of DOM in the overlying water column. Fine-scale water sampling revealed that BP near the sediment (0 – 30 m above the seafloor; 2.78 μmol C m⁻³ d⁻¹) was 1.67 times higher than that measured in the water column above (30 – 100 m above the seafloor; 1.67 μmol C m⁻³ d⁻¹). In addition, BP increased in the bottom water incubation amended with SDOM-containing pore water (PW). The results demonstrated that SDOM contains bio-reactive forms of DOM that stimulate heterotrophic microbial metabolism at the expense of oxygen in the bottom water layer. The accumulation of C1 component in both PW-amended and unamended bottom water incubation (i.e., without an extra DOM supply from sediment) further indicated that refractory DOM is produced autochthonously in the water column via heterotrophic metabolic activity. This explains in part the microbially mediated accumulation of excess FDOMH in the deep-water column of the UB. Overall results suggest that the benthic release of bio-reactive DOM may be of widespread significance in controlling microbial processes in the deep-water layer of marginal seas.
The collection of detailed sampling protocols is crucial tool for the success of the Nansen Legacy, because they ensure: Methodological agreement between the involved researchers Continuity and comparable data throughout the 5 years sampling period An easily accessible overview over parameters sampled Easier cruise planning
Maintaining healthy soils are necessary for developing healthy ecosystems and sustainable agricultural production. It is widely accepted that soil health is a very important management tool to correct unproductive and illness of soil. There is still a lack of clarity about how to measure soil health or what indicators should be taking care of for a satisfying conclusion, considering soil health is not wholly output of soil physical and chemical properties but includes soil biological characteristics. Biological activities mostly occurred in topsoil range up to 30–45 cm soil depth, where most of the soil microbes are living, comprising a tiny portion of about 0.5% of total soil volume and nearly 10% of total soil organic matter. Despite their small population, microbes play a vital role in organic matter decomposition and nitrogen-phosphorus-sulfur cycling. This way soil microbes transformed organic residues into readily available nutrients to plants. They also lead to the degradation/decomposition process of waste materials and some synthetic compounds. Soil microbes produce polysaccharides, which act as soil cementing agent and help in maintaining soil structure, improving aeration and water holding capacity, reducing soil crusting and compaction. Soil microbe shows the capability to assess the integrated measure of soil health, which cannot be achieved through chemical or physical assessment. They respond very quickly to surrounding environmental changes as well as environmental stress conditions. Thus, soil microbes can be an outstanding indicator of soil health. Therefore, there is a need to study on identification, dynamics, and efficiency of soil microbes capable to indicate soil nutrient status or stress conditions, for early signs of soil health improvement or alert to soil degradation. This chapter extensively focuses on the role of soil microbes to indicate soil health status.
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