Ultraviolet-B photodestruction of a light-harvesting complex.

Cyanobacteria are important contributors to global photosynthesis in both marine and terrestrial environments. Quantitative data are presented on UV-B-induced damage to the major cyanobacterial photosynthetic light harvesting complex, the phycobilisome, and to each of its constituent phycobiliproteins. The photodestruction quantum yield, phi295 nm, for the phycobiliproteins is high (approximately 10(-3), as compared with approximately 10(-7) for visible light). Energy transfer on a picosecond time scale does not compete with photodestruction. Photodamage to phycobilisomes in vitro and in living cells is amplified by causing dissociation and loss of function of the complex. In photosynthetic organisms, UV-B damage to light-harvesting complexes may significantly exceed that to DNA.

Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium.

We have cloned the gene for a putative chloroplast RNA polymerase sigma factor from the unicellular rhodophyte Cyanidium caldarium. This gene contains an open reading frame encoding a protein of 609 amino acids with domains highly homologous to all four conserved regions found in bacterial and cyanobacterial sigma 70-type subunits. When Southern blots of genomic DNA were hybridized to the "rpoD box" oligonucleotide probe, up to six hybridizing hands were observed. Transcripts of the sigma factor gene were undetectable in RNA from dark-grown cells but were abundant in the poly(A)+ fraction of RNA from illuminated cells. The sigma factor gene was expressed in Escherichia coli, and antibodies against the expressed sigma factor fusion protein cross-reacted with a 55-kDa protein in partially purified chloroplast RNA polymerase. Antibodies directed against a cyanobacterial RNA polymerase sigma factor also cross-reacted with a 55-kDa protein in the same enzyme preparation. Immunoprecipitation experiments showed that this enzyme preparation contains proteins with the same molecular weights as the alpha, beta, beta', and beta" subunits of chloroplast RNA polymerase in higher plants. This study identifies a gene for a plastid RNA polymerase sigma factor and indicates that there may be a family of nuclear-encoded sigma factors that recognize promoters in subsets of plastid genes and regulate differential gene expression at the transcriptional level.

PipX, the coactivator of NtcA, is a global regulator in cyanobacteria

To modulate the expression of genes involved in nitrogen assimilation, the cyanobacterial PII-interacting protein X (PipX) interacts with the global transcriptional regulator NtcA and the signal transduction protein PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance. PipX can form alternate complexes with NtcA and PII, and these interactions are stimulated and inhibited, respectively, by 2-oxoglutarate, providing a mechanistic link between PII signaling and NtcA-regulated gene expression. Here, we demonstrate that PipX is involved in a much wider interaction network. The effect of pipX alleles on transcript levels was studied by RNA sequencing of S. elongatus strains grown in the presence of either nitrate or ammonium, followed by multivariate analyses of relevant mutant/control comparisons. As a result of this process, 222 genes were classified into six coherent groups of differentially regulated genes, two of which, containing either NtcA-activated or NtcA-repressed genes, provided further insights into the function of NtcA–PipX complexes. The remaining four groups suggest the involvement of PipX in at least three NtcA-independent regulatory pathways. Our results pave the way to uncover new regulatory interactions and mechanisms in the control of gene expression in cyanobacteria.

Stable carbon and oxygen isotope record of live benthic foraminifera from Swedish fjords

In a previous 16-month seasonal study on living (stained) benthic foraminifera from two fjords on the Swedish west coast, it was reported that foraminifera proliferated in response to phytodetritus input; the strongest response came from the opportunistic species Stainforthia fusiformis. In this study, our objective was to find out if that phytodetritus input resulted in a change in the carbon isotopic composition of the foraminiferal tests. We also wanted to examine if variations in salinity and temperature (due to seasonality or deep-water exchanges) were reflected in the delta18O values. From S. fusiformis that were obtained from the Havstens Fjord (20 m) and the Gullmar Fjord (119 m) during the 16-month study, we developed a time series of delta18O and delta13C. After the spring blooms in the Havstens and the Gullmar Fjord, decreases of about 0.2 per mil to 0.3 per mil in the foraminiferal delta13C values were noted; in the Gullmar Fjord after the autumn blooms, decreases of the same order were also noted. Comparing the Havstens and the Gullmar Fjord, we found a 1 per mil difference in both delta13C and delta18O; we attribute this to hydrographic differences between the two fjords. Using calculated values of delta18O, together with the measured ones, we noticed that S. fusiformis in the Gullmar Fjord seems to calcify close to equilibrium with respect to the oxygen isotopes. During autumn, water temperatures were relatively high in the Havstens Fjord, and foraminiferal abundance in the fjord was also high after a phytodetritus input; but, the measured delta18O values do not reflect these higher temperatures. This apparently contradictory combination of results might be explained by a varying delta18O composition of the water during the year, which counterbalances the temperature effect.

Macerals in surface sediments of the Laptev Sea (Arctic Ocean)

Surface sediments from the Laptev Sea and adjacent continental slope were studied for their composition of particulate organic matter (OM) by means of maceral analysis. The composition of macerals in sediments gives information about the environment, terrigenous supply from the hinterland, and marine OM. With reference to their biological sources, we distinguish between terrigenous and marine macerals. We found that the particulate OM in the surface sediments of the Laptev Sea is predominantly of terrigenous origin (mean: 78%). However, distinct variations exist when looking in detail. In the shelf area, sediments may contain up to 99% terrigenous OM. Freshwater algae occur directly north of the river mouths, reflecting the strong fluvial influence. Relatively high amounts of marine OM (20-40%) are restricted to the upper continental slope, the Vilkitsky Strait and west of the New Siberian Islands, explained by increased surface-water productivity due to increased fluvial nutrient supply, open-water conditions, and phytoplankton blooms at the ice-edge.

Sinking rates of particles measured from deployments in the Atlantic Ocean based on seasonal data

The flux of materials to the deep sea is dominated by larger, organic-rich particles with sinking rates varying between a few meters and several hundred meters per day. Mineral ballast may regulate the transfer of organic matter and other components by determining the sinking rates, e.g. via particle density. We calculated particle sinking rates from mass flux patterns and alkenone measurements applying the results of sediment trap experiments from the Atlantic Ocean. We have indication for higher particle sinking rates in carbonate-dominated production systems when considering both regional and seasonal data. During a summer coccolithophorid bloom in the Cape Blanc coastal upwelling off Mauritania, particle sinking rates reached almost 570 m per day, most probably due the fast sedimentation of densely packed zooplankton fecal pellets, which transport high amounts of organic carbon associated with coccoliths to the deep ocean despite rather low production. During the recurring winter-spring blooms off NW Africa and in opal-rich production systems of the Southern Ocean, sinking rates of larger particles, most probably diatom aggregates, showed a tendency to lower values. However, there is no straightforward relationship between carbonate content and particle sinking rates. This could be due to the unknown composition of carbonate and/or the influence of particle size and shape on sinking rates. It also remains noticeable that the highest sinking rates occurred in dust-rich ocean regions off NW Africa, but this issue deserves further detailed field and laboratory investigations. We obtained increasing sinking rates with depth. By using a seven-compartment biogeochemical model, it was shown that the deep ocean organic carbon flux at a mesotrophic sediment trap site off Cape Blanc can be captured fairly well using seasonal variable particle sinking rates. Our model provides a total organic carbon flux of 0.29 Tg per year down to 3000 m off the NW African upwelling region between 5 and 35° N. Simple parameterisations of remineralisation and sinking rates in such models, however, limit their capability in reproducing the flux variation in the water column.

Raw data of SCADCP (self-contained Acoustic Doppler Current Profiler) from three moorings in the Eastern Weddell Sea, 2005-2008

The success of any efforts to determine the effects of climate change on marine ecosystems depends on understanding in the first instance the natural variations, which contemporarily occur on the interannual and shorter time scales. Here we present results on the environmental controls of zooplankton distribution patterns and behaviour in the eastern Weddell Sea, Southern Ocean. Zooplankton abundance and vertical migration are derived from the mean volume backscattering strength (MVBS) and the vertical velocity measured by moored acoustic Doppler current profilers (ADCPs), which were deployed simultaneously at 64°S, 66.5°S and 69°S along the Greenwich Meridian from February, 2005, until March, 2008. While these time series span a period of full three years they resolve hourly changes. A highly persistent behavioural pattern found at all three mooring locations is the synchronous diel vertical migration (DVM) of two distinct groups of zooplankton that migrate between a deep residence depth during daytime and a shallow depth during nighttime. The DVM was closely coupled to the astronomical daylight cycles. However, while the DVM was symmetric around local noon, the annual modulation of the DVM was clearly asymmetric around winter solstice or summer solstice, respectively, at all three mooring sites. DVM at our observation sites persisted throughout winter, even at the highest latitude exposed to the polar night. Since the magnitude as well as the relative rate of change of illumination is minimal at this time, we propose that the ultimate causes of DVM separated from the light-mediated proximal cue that coordinates it. In all three years, a marked change in the migration behaviour occurred in late spring (late October/early November), when DVM ceased. The complete suspension of DVM after early November is possibly caused by the combination of two factors: (1) increased availability of food in the surface mixed layer provided by the phytoplankton spring bloom, and (2) vanishing diurnal enhancement of the threat from visually oriented predators when the illumination is quasi-continuous during the polar and subpolar summer. Zooplankton abundance in the water column, estimated as the mean MVBS in the depth range 50-300 m, was highest end of summer and lowest mid to end winter on the average annual cycle. However, zooplankton abundance varied several-fold between years and between locations. Based on satellite and in situ data of chlorophyll and sea ice as well as on hydrographic measurements, the interannual and spatial variations of zooplankton mean abundance can be explained by differences in the magnitude of the phytoplankton spring bloom, which develops during the seasonal sea ice retreat. Whereas the vernal ice melt appears necessary to stimulate the blooming of phytoplankton, it is not the determinator of the blooms magnitude, its areal extent and duration. A possible explanation for the limitation of the phytoplankton bloom in some years is top-down control. We hypothesise that the phytoplankton spring development can be curbed by grazing when the zooplankton had attained high abundance by growth during the preceding summer.

Thorium-234, POC and PON fluxes during POLARSTERN cruise ANT-XXVIII/3, January-March 2012

Carbon fixation by phytoplankton plays a key role in the uptake of atmospheric CO2 in the Southern Ocean. Yet, it still remains unclear how efficiently the particulate organic carbon (POC) is exported and transferred from ocean surface waters to depth during phytoplankton blooms. In addition, little is known about the processes that control the flux attenuation within the upper twilight zone. Here, we present results of downward POC and particulate organic nitrogen fluxes during the decline of a vast diatom bloom in the Atlantic sector of the Southern Ocean in summer 2012. We used thorium-234 (234Th) as a particle tracer in combination with drifting sediment traps (ST). Their simultaneous use evidenced a sustained high export rate of 234Th at 100 m depth in the weeks prior to and during the sampling period. The entire study area, of approximately 8000 km**2, showed similar vertical export fluxes in spite of the heterogeneity in phytoplankton standing stocks and productivity, indicating a decoupling between production and export. The POC fluxes at 100 m were high, averaging 26 ± 15 mmol C/m**2/d, although the strength of the biological pump was generally low. Only <20% of the daily primary production reached 100 m, presumably due to an active recycling of carbon and nutrients. Pigment analyses indicated that direct sinking of diatoms likely caused the high POC transfer efficiencies (~60%) observed between 100 and 300 m, although faecal pellets and transport of POC linked to zooplankton vertical migration might have also contributed to downward fluxes.

Chlorination for degrading saxitoxins (paralytic shellfish poisons) in water

Chlorination was investigated as a treatment option for degrading and thus removing saxitoxins (paralytic shellfish poisons, PSPs) produced by cyanobacteria (blue-green algae) from water. It was found to be effective with the order of ease of degradation of the saxitoxins being GTX5 (B1) similar to dcSTX > STX > GTX3 similar to C2 > C1 > GTX2. However the effectiveness of chlorine was pH dependent. Degradation as a function of pH was not linear with the degree of degradation increasing rapidly at around pH 7.5. At pH 9 > 90% removal was possible provided a residual of 0.5 mg l(-1) free chlorine was present after 30 min contact time. The more effective degradation at higher pH was unexpected as chlorine is known to be a weaker oxidant under these conditions. The more effective degradation, then, must be due to the toxins, which are ionisable molecules, being present in a form at higher pH which is more susceptible to oxidation. The feasibility of using chlorine to remove saxitoxins during water treatment will therefore depend strongly on the pH of the water being chlorinated. Degradation may be improved by pH adjustment but may not be a practical solution. Although saxitoxins were degraded in that the parent compounds were not detected by chemical analysis, there is no indication as to the nature of the degradation products. However, acute toxicity as determined by the mouse bioassay was eliminated.

Assessing the influence and distribution of shrimp pond effluent in a tidal mangrove creek in north-east Australia

Effluent from a land based shrimp farm was detected in a receiving creek as changes in physical, chemical and biological parameters. The extent and severity of these changes depended on farm operations. This assessment was conducted at three different stages of shrimp-pond maturity, including (1) when the ponds were empty, (2) full and (3) being harvested. Methods for assessing farm effluent in receiving waters included physical/chemical analyses of the water column, phytoplankton bioassays and nitrogen isotope signatures of marine flora. Comparisons were made with an adjacent creek that served as the farms intake creek and did not directly receive effluent. Physical/chemical parameters identified distinct changes in the receiving creek with respect to farm operations. Elevated water column NH4+ (18.5+/-8.0 muM) and chlorophyll a concentrations (5.5+/-1.9 mug/l) were measured when the farm was in operation, in contrast to when the farm was inactive (1.3+/-0.3 muM and 1.2+/-0.6 mug/l, respectively). At all times, physically chemical parameters at the mouth of the effluent creek, were equivalent to control values, indicating effluent was contained within the effluent-receiving creek. However, elevated delta(15)N signatures of mangroves (up to similar to8parts per thousand) and macroalgae (up to similar to5parts per thousand) indicated a broader influence of shrimp farm effluent, extending to the lower regions of the farms intake creek. Bioassays at upstream sites close to the location of farm effluent discharge indicated that phytoplankton at these sites did not respond to further nutrient additions, however downstream sites showed large growth responses. This suggested that further nutrient loading from the shrimp farm, resulting in greater nutrient dispersal, will increase the extent of phytoplankton blooms downstream from the site of effluent discharge. When shrimp ponds were empty water quality in the effluent and intake creeks was comparable. This indicated that observed elevated nutrient and phytoplankton concentrations were directly attributable to farm operations. (C) 2003 Elsevier Ltd. All rights reserved.

Disruption of the BLM gene in ATM-null DT40 cells does not exacerbate either phenotype

Bloom syndrome and ataxia-telangiectasia are autosomal recessive human disorders characterized by immunodeficiency, genome instability and predisposition to develop cancer. Recent data reveal that the products of these two genes, BLM and ATM, interact and function together in recognizing abnormal DNA structures. To investigate the function of these two molecules in DNA damage recognition, we generated double knockouts of ATM(-/-) BLM-/- in the DT40 chicken B-lymphocyte cell line. The double mutant cells were viable and exhibited a variety of characteristics of both ATM(-/-) and BLM-/- cells. There was no evidence for exacerbation of either phenotype; however, the more extreme radiosensitivity seen in ATM(-/-) and the elevated sister chromatid exchange seen in BLM-/- cells were retained in the double mutants. These results suggest that ATM and BLM have largely distinct roles in recognizing different forms of damage in DNA, but are also compatible with partially overlapping functions in recognizing breaks in radiation-damaged DNA.

Morphological changes during akinete germination in Cylindrospermopsis raciborskii (Nostocales, Cyanobacteria)

The occurrence of the cyanobacterium Cylindrospermopsis raciborskii (Woloszynska) Seenayya and Subba Raju is a global water quality issue. The misidentification of C. raciborskii in the past is a major concern for water quality users, considering the reported cases of human and livestock poisonings associated with the cyanobacterium. Many of the available taxonomic descriptions for this species provide little or no detail of the morphology of early developmental phases that may assist with identification. Therefore, typifying the morphological changes throughout the entire life cycle for such a species requires urgent attention. In this study, five distinct morphological phases identified using a new culturing technique are reported for the process of akinete germination in C. raciborskii. Before the terminal emergence of three to four cell germlings through a ruptured akinete envelope (phase 3), mature akinetes (phase 1) elongated and the endospore separated from the akinete envelope (phase 2). After the association with the envelope was lost, four-cell germlings (phase 4a) matured into young trichomes of more than four cells (phase 4b). Throughout the process of germination, internal granular structures decreased in size and were irregular in shape in germlings and young trichomes. The culturing technique, which used a Sedgwick-Rafter cell, was successful in its application but was limiting in that the development of young trichomes after phase 4b could not be monitored.

Anomalous magnetic susceptibility values and traces of subsurface microbial activity in carbonate banks on San Salvador Island, Bahamas

Pure limestones beneath the paleosols on San Salvador Island, Bahamas, contain strong positive magnetic susceptibility anomalies, although the iron content is generally very low. These magnetic phenomena differ from those associated with disconformities, which are marked by accumulation of paramagnetic airborne dust deposits with relatively high iron content. The strength and characters of the magnetic response in these subsurface zones correspond to the presence of magnetite, particularly small single-domain magnetite crystals of microbial origin. These crystals are not present elsewhere in the intergranular rock pores or microvugs. They are preferentially concentrated in capillary microborings, which developed concurrently with formation of calcite cements that have soil-related C and O isotope compositions. These magnetic zones occur several meters below the overlying soil horizons. Very thin and long linear microborings may be attributable to cyanobacterial microborers. The single-domain magnetites in these micrometer-size tunnels plugged by calcite appear to result from later occupation of these tiny holes by magnetotactic bacteria. Inorganic origin of the magnetite seems unlikely. Numerous traces that suggest subsurface microbial activity provide evidence that may be used to develop possible scenarios for subsequent biological studies of the precise bacteria involved.