Archive for September, 2015

Survival and expression of DNA repair genes in marine bacteria Pseudomonas pseudoalcaligenes NP103 and P. aeruginosa N6P6 in response to environmental stressors

A comparative response of marine bacteria Pseudomonas pseudoalcaligenes NP103 and P. aeruginosa N6P6 under pH stress and UV radiation (UVR) revealed that both their survival pattern and repair mechanism are species specific. In case of P. pseudoalcaligenes NP103, the survival was maximum at pH 8, which decreased with decline in pH of the medium. Whereas, in P. aeruginosa N6P6, maximum survival was observed at pH 7. On exposure to UVR at different doses (25–200 mJ/cm2) and increasing concentrations of Na+ (1–6%), considerable differences in the recovery (2% for P. pseudoalcaligenes NP103 and 3% for P. aeruginosa N6P6) from UVR induced damage was observed. The qRT-PCR analysis of DNA repair genes (recA and uvrA) of marine bacteria subjected to different pH conditions showed significant (P < 0.05) up-regulation of both genes at pH 6, indicating higher degree of DNA damage at low pH. Furthermore, exposure of UVR irradiated cell suspensions to visible light exhibited greater photo-reactivating capacity in P. pseudoalcaligenes NP103 as compared to P. aeruginosa N6P6. The present findings indicate that pH and UVR exposure have crucial role in dictating the light dependent and independent DNA repair pathway in marine bacteria. Further, we speculate that both these repair response to the environmental stressors varies with bacterial species.

Continue reading ‘Survival and expression of DNA repair genes in marine bacteria Pseudomonas pseudoalcaligenes NP103 and P. aeruginosa N6P6 in response to environmental stressors’

The marine carbonate system of the Arctic Ocean: Assessment of internal consistency and sampling considerations, summer 2010

The Arctic Ocean has experienced tremendous changes in recent years. To evaluate temporal and spatial variations of the marine carbonate system, a rigorous evaluation of the quality and internal consistency of Arctic field data and the applicability of existing thermodynamic constants to Arctic conditions is needed. Low Arctic temperatures fall outside the range of conditions used to experimentally determine these constants. Using data collected during the Chinese National Arctic Research Expedition (CHINARE) cruise of summer 2010, we compared underway measurements of the partial pressure of carbon dioxide (pCO2) to pCO2 values calculated using measurements of dissolved inorganic carbon (DIC) and total alkalinity (TAlk) and seven sets of dissociation constants. For waters sampled outside areas of active sea ice melt, calculated and measured pCO2 values agreed best when the calculations incorporated the carbonic acid dissociation constants of Mehrbach et al. (1973) (as refit by Dickson and Millero (1987)) (mean difference of 1.5 μatm ± standard deviation of 5.7 μatm) or Lueker et al. (2000) (2.3 ± 5.4 μatm). Differences between calculated and measured pCO2 values were related to temperature and salinity and were, for all sets of constants, increasing with increasing T and S over a temperature range of − 1.5 to 10.5 °C and a salinity range of 25.8 to 33.1. In the relatively warm Bering Sea, calculated pCO2 was higher than measured pCO2, but in the colder Canada Basin, calculated values were lower than measured values. This pattern indicates that calculations of pCO2 in very cold waters may underestimate pCO2, with an uncertainty of ~ 5 μatm in accuracy. In areas of active sea ice melt (ice cover < 35%), large differences between calculated and measured pCO2 values occurred. We explored possible explanations for these large differences and concluded that dissolution of CaCO3 precipitates from sea ice in samples is the most likely cause. Further research including a comparison of filtered and unfiltered samples is needed to resolve this issue. Many processes influence the marine carbonate system of the Arctic Ocean, and further assessment of their relative roles is needed.

Continue reading ‘The marine carbonate system of the Arctic Ocean: Assessment of internal consistency and sampling considerations, summer 2010’

Shell suspends Arctic exploration; acidification already ravaging oceans (audio & text)

(…) The vast and pristine Arctic region is already feeling the devastating affects of climate change on retreating glaciers, thawing permafrost and eroding shorelines.

But as FSRN’s Seán Kinane reports, there’s another consequence of skyrocketing levels of carbon dioxide in the atmosphere: ocean acidification.

The concentration of carbon dioxide in the atmosphere is at levels not seen in a million years and it’s not just warming the air and water, it’s causing oceans to acidify. Erinn Muller manages Mote Marine Laboratory’s coral disease and health program in Sarasota, Florida.

Continue reading ‘Shell suspends Arctic exploration; acidification already ravaging oceans (audio & text)’

Global review of the Permian–Triassic mass extinction and subsequent recovery: Part II

The present volume represents Part II of a thematic issue of Earth-Science Reviews titled “Global Review of the Permian-Triassic Mass Extinction and Subsequent Recovery”. Part I of this thematic issue was published in May 2014 as Earth-Science Reviews Volume 137 (see Chen et al., 2014). The nine studies in the present volume rely extensively on research undertaken in the context of IGCP Project 572 (“Restoration of Marine Ecosystems following the Permian-Triassic Mass Extinction: Lessons for the Present”), which brought together a large number of geoscientists from around the world for a series of field workshops, meetings, and symposia from 2008 to 2014. IGCP 572 members published an average of ~ 120 research papers annually, with many studies contributing to a better understanding of the mechanisms and causes of the PTB biocrisis and the protracted recovery that followed it. This project yielded eight journal special issues prior to the two Earth-Science Reviews volumes ( Algeo et al., 2011b, Algeo et al., 2013a, Chen et al., 2009, Chen et al., 2013, Crasquin, 2013, Heydari et al., 2010, Metcalfe and Isozaki, 2009 and Xie and Kershaw, 2012). A successor project, IGCP 630 (“Permian-Triassic Climatic and Environmental Extremes and Biotic Response”) was initiated in 2014 and will run through 2019. Its principal goals are to better understand (1) connections between extreme warming, environmental changes, and contemporaneous biotic decline and recovery, and (2) interactions between terrestrial and marine ecosystems and their interdependent response to large-scale climate and environmental changes. (…)

Continue reading ‘Global review of the Permian–Triassic mass extinction and subsequent recovery: Part II’

Growth rate analysis and protein identification of Kappaphycus alvarezii (Rhodophyta, Gigartinales) under pH induced stress culture

Environmental pH is one of the factors contributing to abiotic stress which in turn influences the growth and development of macroalgae. This study was conducted in order to assess the growth and physiological changes in Kappaphycus alvarezii under different pH conditions: pHs 6, ∼8.4 (control) and 9. K. alvarezii explants exhibited a difference in the daily growth rate (DGR) among the different pH treatments (p ≤ 0.05). The highest DGR was observed in control culture with pH ∼8.4 followed by alkaline (pH 9) and acidic (pH 6) induced stress cultures. Protein expression profile was generated from different pH induced K. alvarezii cultures using sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by protein identification and analysis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) and Mascot software. Ribulose bisphosphate carboxylase (Rubisco) large chain was identified to be up-regulated under acidic (pH 6) condition during the second and fourth week of culture. The findings indicated that Rubisco can be employed as a biomarker for pH induced abiotic stress. Further study on the association between the expression levels of Rubisco large chain and their underlying mechanisms under pH stress conditions is recommended.

Continue reading ‘Growth rate analysis and protein identification of Kappaphycus alvarezii (Rhodophyta, Gigartinales) under pH induced stress culture’

Characterisation and deployment of an immobilised pH sensor spot towards surface ocean pH measurements

The oceans are a major sink for anthropogenic atmospheric carbon dioxide, and the uptake causes changes to the marine carbonate system and has wide ranging effects on flora and fauna. It is crucial to develop analytical systems that allow us to follow the increase in oceanic pCO2 and corresponding reduction in pH. Miniaturised sensor systems using immobilised fluorescence indicator spots are attractive for this purpose because of their simple design and low power requirements. The technology is increasingly used for oceanic dissolved oxygen measurements.

We present a detailed method on the use of immobilised fluorescence indicator spots to determine pH in ocean waters across the pH range 7.6–8.2. We characterised temperature (−0.046 pH/°C from 5 to 25 °C) and salinity dependences (−0.01 pH/psu over 5–35), and performed a preliminary investigation into the influence of chlorophyll on the pH measurement. The apparent pKa of the sensor spots was 6.93 at 20 °C. A drift of 0.00014 R (ca. 0.0004 pH, at 25 °C, salinity 35) was observed over a 3 day period in a laboratory based drift experiment. We achieved a precision of 0.0074 pH units, and observed a drift of 0.06 pH units during a test deployment of 5 week duration in the Southern Ocean as an underway surface ocean sensor, which was corrected for using certified reference materials. The temperature and salinity dependences were accounted for with the algorithm, R=0.00034−0.17·pH+0.15·S2+0.0067·T−0.0084·S·1.075R=0.00034−0.17·pH+0.15·S2+0.0067·T−0.0084·S·1.075.

This study provides a first step towards a pH optode system suitable for autonomous deployment. The use of a short duration low power illumination (LED current 0.2 mA, 5 μs illumination time) improved the lifetime and precision of the spot. Further improvements to the pH indicator spot operations include regular application of certified reference materials for drift correction and cross-calibration against a spectrophotometric pH system. Desirable future developments should involve novel fluorescence spots with improved response time and apparent pKa values closer to the pH of surface ocean waters.

Continue reading ‘Characterisation and deployment of an immobilised pH sensor spot towards surface ocean pH measurements’

Cold-water fishes and climate change in North America

Trout, salmon, grayling and whitefishes (Salmonidae) are among the most ecologically and economically important fishes. They also are among the most vulnerable to global warming, and increasing drought, floods, and wildfires. In North America, salmonids occur from central Mexico northward along coastal regions and mountainous interiors to the Arctic Plains. A variety of existing stressors have reduced population sizes and extent and fragmented habitats, making salmonid populations increasingly vulnerable to climate-driven disturbances. This contribution explores specific threats posed by climate change and suggests actions that can help these coldwater-dependent species adapt to an increasingly warm and uncertain future.

Continue reading ‘Cold-water fishes and climate change in North America’

Carbonic anhydrase activity changes in response to increased temperature and pCO2 in Symbiodinium–zoanthid associations

Carbon dioxide (CO2) makes up less than 1% of dissolved inorganic carbon (DIC) in the ocean. To acquire carbon dioxide for photosynthesis, many marine autotrophs rely on the enzyme carbonic anhydrase (CA) to catalyze the conversion of bicarbonate ions (HCO3−) to CO2. In zoanthids and other cnidarians with Symbiodinium spp. endosymbionts, CA is essential for transporting CO2 to symbionts for photosynthesis. Temperature and ambient DIC affect CA activity, therefore, increased sea water temperatures and ocean acidification (OA) will alter CO2 transport in symbiotic cnidarians. However, these effects are likely to be species specific for both host and symbiont, as different cnidarians and Symbiodinium spp. vary in their mechanisms of DIC transport and utilization of CA. In this study, host and symbiont CA activity in the zoanthids Palythoa sp. and Zoanthus sp. varied with thermal stress and low pH. Increased temperature inhibited algal, but not host CA activity in Zoanthus sp. polyps with A4 Symbiodinium, while temperature had no effect on CA activity in Palythoa sp. with C1 Symbiodinium. High pCO2/low pH altered algal CA activity in both zoanthid species, but host CA activity changed in Zoanthus sp. polyps only. This study shows that thermal stress and OA induce species-specific changes in CA activity, and thus DIC transport in symbiotic zoanthids. These observations suggest that CA activity in symbiotic cnidarians will be altered by climate conditions predicted for the future, and for some cnidarians, changes in CA activity may inhibit photosynthesis.

Continue reading ‘Carbonic anhydrase activity changes in response to increased temperature and pCO2 in Symbiodinium–zoanthid associations’

Ocean acidification modulates expression of genes and physiological performance of a marine diatom

Ocean Acidification (OA) is known to affect various aspects of the physiological performance of diatoms, but there is little information on the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum expression of the genes related to light harvesting, carbon acquisition and carboxylation, nitrite assimilation and ATP synthesis are modulated by OA. Growth and photosynthetic carbon fixation were enhanced by elevated CO2 (1000 μatm) under both constant indoor and fluctuating outdoor light regimes. The genetic expression of nitrite reductase (NiR) was up-regulated by OA regardless of light levels and/or regimes. The transcriptional expression of fucoxanthin chlorophyll a/c protein (lhcf type (FCP)) and mitochondrial ATP synthase (mtATP synthase) genes were also enhanced by OA, but only under high light intensity. OA treatment decreased the expression of β-carbonic anhydrase (β-CA) along with down-regulation of CO2 concentrating mechanisms (CCMs). Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expressions either under constant indoor light or fluctuating sunlight. Thus, OA enhanced photosynthetic and growth rates by stimulating nitrogen assimilation and indirectly by down-regulating the energy-costly inorganic carbon acquisition process.

Continue reading ‘Ocean acidification modulates expression of genes and physiological performance of a marine diatom’

Vanishing coccolith vital effects with alleviated CO2 limitation

By recreating a range of geologically relevant concentrations of dissolved inorganic carbon (DIC) in the laboratory, we demonstrate that the magnitude of the vital effects in both carbon and oxygen isotopes of coccolith calcite of multiple species relates to ambient DIC concentration. Under high DIC levels, all the examined coccoliths lacked any offset from inorganic calcite, whereas in low (present-day) DIC concentrations, these vital effects and interspecies differences become substantial. These laboratory observations support the recent hypothesis from field observations that the appearance of interspecific vital effect in coccolithophores coincides with the long-term Neogene decline of atmospheric CO2 concentrations. The present study brings further valuable constraints on coccolith isotopic compositions by demonstrating the threshold for the absence of vital effects under high DIC regimes. From a mechanistic viewpoint, we show that the vital effect is determined by physiology; growth rate, cell size and relative rates of photosynthesis and calcification, and a modulation of these parameters with ambient carbon availability. This study provides palaeoceanographers with a biogeochemical framework that can be utilised to further develop the use of calcareous nannofossils in palaeoceanography to derive sea surface temperature and pCO2 levels.

Continue reading ‘Vanishing coccolith vital effects with alleviated CO2 limitation’

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Ocean acidification in the IPCC AR5 WG II

OUP book