ALBERT

Description: Meiobenthos densities and higher taxon composition were studied in an active gas seepage area at depths from 182 to 252 m in the submarine Dnieper Canyon located in the northwestern part of the Black Sea. The meiobenthos was represented by Ciliata, Foraminifera, Nematoda, Polychaeta, Bivalvia, Gastropoda, Amphipoda, and Acarina. Also present in the sediment samples were juvenile stages of Copepoda and Cladocera which may be of planktonic origin. Nematoda and Foraminifera were the dominant groups. The abundance of the meiobenthos varied between 2397 and 52,593 ind.·m−2. Maximum densities of Nematoda and Foraminifera were recorded in the upper sediment layer of a permanent H2S zone at depths from 220 to 250 m. This dense concentration of meiobenthos was found in an area where intense methane seeps were covered by methane-oxidizing microbial mats. Results suggest that methane and its microbial oxidation products are the factors responsible for the presence of a highly sulfidic and biologically productive zone characterized by specially adapted benthic groups. At the same time, an inverse correlation was found between meiofauna densities and methane concentrations in the uppermost sediment layers. The hypothesis is that the concentration of Nematoda and Foraminifera within the areas enriched with methane is an ecological compromise between the food requirements of these organisms and their adaptations to the toxic H2S.

Description: The deep anoxic shelf of the northwestern Black Sea has numerous gas seeps, which are populated by methanotrophic microbial mats in and above the seafloor. Above the seafloor, the mats can form tall reef-like structures composed of porous carbonate and microbial biomass. Here, we investigated the spatial patterns of CH4 and CO2 assimilation in relation to the distribution of ANME groups and their associated bacteria in mat samples obtained from the surface of a large reef structure. A combination of different methods, including radiotracer incubation, beta microimaging, secondary ion mass spectrometry, and catalyzed reporter deposition fluorescence in situ hybridization, was applied to sections of mat obtained from the large reef structure to locate hot spots of methanotrophy and to identify the responsible microbial consortia. In addition, CO2 reduction to methane was investigated in the presence or absence of methane, sulfate, and hydrogen. The mat had an average δ13C carbon isotopic signature of −67.1‰, indicating that methane was the main carbon source. Regions dominated by ANME-1 had isotope signatures that were significantly heavier (−66.4‰ ± 3.9 ‰ [mean ± standard deviation; n = 7]) than those of the more central regions dominated by ANME-2 (−72.9‰ ± 2.2 ‰; n = 7). Incorporation of 14C from radiolabeled CH4 or CO2 revealed one hot spot for methanotrophy and CO2 fixation close to the surface of the mat and a low assimilation efficiency (1 to 2% of methane oxidized). Replicate incubations of the mat with 14CH4 or 14CO2 revealed that there was interconversion of CH4 and CO2. The level of CO2 reduction was about 10% of the level of anaerobic oxidation of methane. However, since considerable methane formation was observed only in the presence of methane and sulfate, the process appeared to be a rereaction of anaerobic oxidation of methane rather than net methanogenesis.

Description: Force chain buckling, leading to unjamming and shear banding, is examined quantitatively via a discrete element analysis of a two-dimensional, densely-packed, cohesionless granular assembly subject to quasistatic, boundary-driven biaxial compression. A range of properties associated with the confined buckling of force chains has been established, including: degree of buckling, buckling modes, spatial and strain evolution distributions, and relative contributions to non-affine deformation, dilatation and decrease in macroscopic shear strength and potential energy. Consecutive cycles of unjamming–jamming events, akin to slip–stick events arising in other granular systems, characterize the strain-softening regime and the shear band evolution. Peaks in the dissipation rate, kinetic energy and local non-affine strain are strongly correlated: the largest peaks coincide with each unjamming event that is evident in the concurrent drops in the macroscopic shear stress and potential energy. Unjamming nucleates from the buckling of a few force chains within a small region inside the band. A specific mode of force chain buckling, prevalent in and confined to the shear band, leads to above-average levels of local non-affine strain and release of potential energy during unjamming. Ongoing studies of this and other buckling modes from a structural stability standpoint serve as the basis for the formulation of internal variables and associated evolution laws, central to the development of thermomicromechanical constitutive theory for granular materials.

Description: A simple unified critical state constitutive model for bonded geomaterials is presented in this paper. The model, which is called CASM-n, is an enhancement of an existing unified critical state model for reconstituted geomaterials (CASM). Characteristic behaviours of a bonded geomaterial such as the pre-yield higher strength and stiffness and the cohesive–frictional shearing mode in the post-yield region are taken into account and included in the reference model. The salient feature of the proposed model is the incorporation of cohesive component into the stress–dilatancy relationship. Consideration of the contribution of cohesion to plastic flow allows the modelling of delayed dilatancy and softening–contraction behaviour, which are two interesting phenomena observed in bonded geomaterials.

Description: Diosmetin, 5,7,3′-trihydroxy-4′-methoxyflavone shows chemopreventive, antimutagenic, and antiallergic effects. On the other hand, chrysoeriol, 5,7,4′-trihydroxy-3′-methoxyflavone induced nodABC-lacZ in Rhizobium meliloti. Both of them belong to hydroxymethoxy- flavones. One major difference between diosmetin and chrysoeriol is the substituted position of hydroxyl and methoxyl groups. In order to elucidate the relationships between their structures and activity, one of the first things to be done is the determination of their structures. However, most flavones occur widely in nature, and thus it is difficult to obtain in sufficient amounts from natural sources to identify their structures. Assignments of NMR data of several hydroxymethoxyflavones may help us to identify novel flavonoid compounds isolated from natural sources based on their NMR experiments. Therefore, we report here the complete assignments of 1H and 13C NMR data of 13 hydroxymethoxyflavones.

Description: Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a high spatial resolution analytical method which has been applied to the analysis of silicic tephras. With current instrumentation, around 30 trace elements can be determined from single glass shards as small as ∼ 40 µm, separated from tephra deposits. As a result of element fractionation during the ablation process using a 266 nm laser, a relatively complex calibration strategy is required. Nonetheless, such a strategy gives analyses which are accurate (typically within ±5%) and have an analytical precision which varies from ∼ ±2% at 100 ppm, to ∼ ±15% at 1 ppm. Detection limits for elements used in correlation and discrimination studies are well below 1 ppm. Examples of the application of trace element analysis by LA-ICP-MS in tephra studies are presented from the USA, New Zealand and the Mediterranean. Improvements in instrumental sensitivity in recent years have the potential to lower detection limits and improve analytical precision, thus allowing the analysis of smaller glass shards from more distal tephras. Laser systems operating at shorter wavelengths (e.g. 193 nm) are now more widely available, and produce a much more controllable ablation in glasses than 266 nm lasers. Crater sizes of 〈10 µm are easily achieved, and at 193 nm many of the elemental fractionation issues which mar longer wavelengths are overcome. By coupling a short wavelength laser to a modern ICP-MS it should be possible to determine the trace element composition of glass shards as small as 20 µm and, providing sample preparation issues can be overcome, the determination of the more abundant trace elements in glass shards as small as 10 µm is within instrumental capabilities. This will make it possible to chemically fingerprint tephra deposits which are far from their sources, and will greatly extend the range over which geochemical correlation of tephras can be undertaken.

Description: Many marine demosponges contain large amounts of phylogenetically complex yet highly sponge-specific microbial consortia within the mesohyl matrix, but little is known about how these microorganisms are acquired by their hosts. Settlement experiments were performed with the viviparous Caribbean demosponge Ircinia felix to investigate the role of larvae in the vertical transmission of the sponge-associated microbial community. Inspections by electron microscopy revealed large amounts of morphologically diverse microorganisms in the center of I. felix larvae, while the outer rim appeared to be devoid of microorganisms. In juveniles, microorganisms were found between densely packed sponge cells. Denaturing gradient gel electrophoresis (DGGE) was performed to compare the bacterial community profiles of adults, larvae, and juvenile sponges. Adults and larvae were highly similar in DGGE band numbers and banding patterns. Larvae released by the same adult individual contained highly similar DGGE banding patterns, whereas larvae released by different adult individuals showed slightly different DGGE banding patterns. Over 200 bands were excised, sequenced, and phylogenetically analyzed. The bacterial diversity of adult I. felix and its larvae was comparably high, while juveniles showed reduced diversity. In total, 13 vertically transmitted sequence clusters, hereafter termed “IF clusters,” that contained sequences from both the adult sponge and offspring (larvae and/or juveniles) were found. The IF clusters belonged to at least four different eubacterial phyla and one possibly novel eubacterial lineage. In summary, it could be shown that in I. felix, vertical transmission of microorganisms through the larvae is an important mechanism for the establishment of the sponge-microbe association.

Description: Numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid genes were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping genes, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS genes from complex sponge-symbiont associations.

Description: Tropical cyclones (TC) under different climate conditions in the Northern Hemisphere have been investigated with the Max Planck Institute (MPI) coupled (ECHAM5/MPI-OM) and atmosphere (ECHAM5) climate models. The intensity and size of the TC depend crucially on resolution with higher wind speed and smaller scales at the higher resolutions. The typical size of the TC is reduced by a factor of 2.3 from T63 to T319 using the distance of the maximum wind speed from the centre of the storm as a measure. The full three-dimensional structure of the storms becomes increasingly more realistic as the resolution is increased. For the T63 resolution, three ensemble runs are explored for the period 1860 until 2100 using the IPCC SRES scenario A1B and evaluated for three 30 yr periods at the end of the 19th, 20th and 21st century, respectively. While there is no significant change between the 19th and the 20th century, there is a considerable reduction in the number of the TC by some 20% in the 21st century, but no change in the number of the more intense storms. Reduction in the number of storms occurs in all regions. A single additional experiment at T213 resolution was run for the two latter 30-yr periods. The T213 is an atmospheric only experiment using the transient sea surface temperatures (SST) of the T63 resolution experiment. Also in this case, there is a reduction by some 10% in the number of simulated TC in the 21st century compared to the 20th century but a marked increase in the number of intense storms. The number of storms with maximum wind speeds greater than 50 m s−1 increases by a third. Most of the intensification takes place in the Eastern Pacific and in the Atlantic where also the number of storms more or less stays the same. We identify two competing processes effecting TC in a warmer climate. First, the increase in the static stability and the reduced vertical circulation is suggested to contribute to the reduction in the number of storms. Second, the increase in temperature and water vapour provide more energy for the storms so that when favourable conditions occur, the higher SST and higher specific humidity will contribute to more intense storms. As the maximum intensity depends crucially on resolution, this will require higher resolution to have its full effect. The distribution of storms between different regions does not, at first approximation, depend on the temperature itself but on the distribution of the SST anomalies and their influence on the atmospheric circulation. Two additional transient experiments at T319 resolution where run for 20 yr at the end of the 20th and 21st century, respectively, using the same conditions as in the T213 experiments. The results are consistent with the T213 study. The total number of TC were similar to the T213 experiment but were generally more intense. The change from the 20th to the 21st century was also similar with fewer TC in total but with more intense cyclones.

Description: Ignicoccus hospitalis is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon, Nanoarchaeum equitans. In this study, the biosynthetic pathways of I. hospitalis were investigated by in vitro enzymatic analyses, in vivo 13C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO2 fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO2 acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvate-ferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarate-oxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the α-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of I. hospitalis revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.

Description: Natural communities are constantly changing due to a variety of interacting external processes and the temporal occurrence and intensity of these processes can have important implications for the diversity and structure of marine sessile assemblages. In this study, we investigated the effects of temporal variation in a disturbance regime, as well as the specific timing of events within different regimes, on the composition and diversity of marine subtidal fouling assemblages. We did this in a multi-factorial experiment using artificial settlement tiles deployed at two sites on the North East coast of England. We found that although there were significant effects of disturbances on the composition of assemblages, there were no effects of either the variation in the disturbance regime or the specific timing of events on the diversity or assemblage composition at either site. In contrast to recent implications we conclude that in marine fouling assemblages, the variability in disturbance regimes (as a driving force) is unimportant, while disturbance itself is an important force for structuring robust ecosystems.

Description: The measurements of dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) in seawater are key in global change and coastal eutrophication studies. Nowadays, the high-temperature combustion (HTC) technique is a widely used method for DOC and TDN analysis. However, uncertainties exist about the operation of the catalyst in the conversion process of DOC and TDN in the HTC method. In this study, five different 'catalyst' materials were tested for their blanks, calibration slopes, and conversion efficiency of DOC and TDN using the Shimadzu TOC 5000A total organic carbon analyser coupled to a Sievers NCD 255 nitrogen chemiluminescence detector. The materials included four metallic catalysts (Shimadzu and Johnson 0.5 Pt-alumina, 13 Cu(II)O-alumina, 0.5 Pd-alumina) and quartz beads. The results indicated that DOC blank signals for the HTC approach using metallic catalysts with an alumina support are higher compared with quartz beads, as a result of the amphoteric nature of the alumina. However, the slopes of the standard calibration graphs were lowest for DOC and TDN determinations on the quartz beads. The DOC recoveries for the metallic catalysts were close to 100 for all compounds tested, with the exception of ammonium pyrrolidine dithiocarbamate. Using quartz beads, poor recoveries were obtained for a range of organic compounds, including the commonly used calibration compounds potassium hydrogen phthalate and glycine. The TDN recoveries for all compounds were typically >90, with the exception of NaNO2. Furthermore, analysis using the CuO-alumina and Pd-alumina catalysts and quartz beads showed low recoveries for NH4Cl. This study showed that catalyst performance should be verified on a regular basis using model compounds and blank checks made during every run, and that the Shimadzu 0.5 Pt-alumina material was an efficient catalyst for DOC and TDN analyses using the coupled total organic carbon-nitrogen chemiluminescence detector (TOC-NCD) analyser. © 2007 Taylor & Francis.

Description: Data from two cross-shelf sediment sampling cruises were used to explain reasons for the sediment biogeochemical variability in respect of carbon, nitrogen and sulphur, and how the cycling of these elements governs the biogeochemistry of the overlying water through their control of the redox conditions. The spatial extent of this benthic–pelagic flux link is limited to the innershelf mud belt system on the Namibian shelf. The inshore mud belt is the primary deposition area of the carbon and nitrogen new production export flux. The offshore organic-rich zones are thought to be relict particulate organic matter originating from the inshore mud belt rather than from an overlying pelagic source. These data were used to set up a multi-layer sediment model that was used through sensitivity analyses to elucidate the input characteristics that result in the most significant feedbacks on hypoxia in the overlying water. The analyses showed that, although the new production flux is a requirement to drive an oxygen demand in the sediments, the onset and persistence of anoxia may depend critically on a low-oxygen boundary condition threshold. This is thought to be a key differentiating factor between systems that, despite comparable carbon export fluxes, are characterised by a persistent hypoxia/anoxia signal and those that are characterised by episodic hypoxia events. It was concluded that sediment oxygen demand and methane and 'sulphide' emissions from the central Benguela sediments are responses to external hypoxia boundary conditions rather than the local drivers of oxygen variability.

Description: The functional response of Sepia officinalis early stages, preying on mysids of the species Mesopodopsis slabberi was investigated. The effects of five prey densities (12.5, 25, 37.5, 50 and 125 mysids l−1) and two hatchling ages (1-day-old and 7-day-old) on consumption rate and the frequency of non-feeding animals were tested. Older animals were approximately 50% heavier than newly hatched ones. Hatchlings were individually assayed under 0.25 W m−2 natural light, 37.8 psu in salinity and 19°C. The effect of prey density on consumption rate was highly significant and no effect of age was detected within the age range tested. Maximal values recorded for consumption rate were about 0.45 mysids h−1. The frequency of non-feeding individuals was strongly reduced at saturating prey densities. The functional response curve showed an interval of prey densities for which density-dependent prey mortality is probable.

Description: We report data on the stomach contents of the long‐finned pilot whale, Globicephala melas, recovered from a group of whales stranded on Ruakaka Beach, northeastern New Zealand, in November 2006. In nine whales for which identifiable stomach contents were recovered (three that stranded on 10 November and six that stranded on 11 November) prey remains comprised exclusively cephalopod beaks attributed to five squid species. The stomachs of a further two whales contained unidentifiable upper beaks only, while the stomachs of five whales were completely empty. No whale appeared to have been satiated immediately before stranding, given that the maximum biomass of prey recently consumed by any one whale was calculated to be 〈5 kg. All squids ingested represented oceanic species, found from 50 to 1000 m but more common towards the deeper end of this range. These data both complement and contrast with the only other dietary information available for this species in New Zealand waters, reported from stomach contents of whales stranded on Farewell Spit, South Island in December 2005.

Description: Stomach contents of the long‐finned pilot whale, Globicephala melas, are reported for the first time from New Zealand waters. Analyses based on two male and three female whales (2.5–5.3 m in length) that stranded on Farewell Spit, Golden Bay, South Island in December 2005 revealed a diet comprised exclusively of cephalopods (2-33 lower cephalopod beaks per stomach). Two genera of cephalopod from two orders; arrow squid, Nototodarus spp. (Teuthoidea: Ommastrephidae), and common octopus, Pinnoctopus cordiformis (Octopoda: Octopodidae) were represented. A further five pilot whale stomachs were examined and found to be empty.

Description: A Synechococcus sp. strain PCC 7002 Fe bioreporter was constructed containing the isiAB promoter fused to the Vibrio harveyi luxAB genes. Bioreporter luminescence was characterized with respect to the free ferric ion concentration in trace metal-buffered synthetic medium. The applicability of the Fe bioreporter to assess Fe availability in the natural environment was tested by using samples collected from the Baltic Sea and from the high-nutrient, low-chlorophyll subarctic Pacific Ocean. Parallel assessment of dissolved Fe and bioreporter response confirmed that direct chemical measurements of dissolved Fe should not be considered alone when assessing Fe availability to phytoplankton.

Description: The hyperthermophilic archaeon Archaeoglobus fulgidus strain 7324 has been shown to grow on starch and sulfate and thus represents the first sulfate reducer able to degrade polymeric sugars. The enzymes involved in starch degradation to glucose 6-phosphate were studied. In extracts of starch-grown cells the activities of the classical starch degradation enzymes, α-amylase and amylopullulanase, could not be detected. Instead, evidence is presented here that A. fulgidus utilizes an unusual pathway of starch degradation involving cyclodextrins as intermediates. The pathway comprises the combined action of an extracellular cyclodextrin glucanotransferase (CGTase) converting starch to cyclodextrins and the intracellular conversion of cyclodextrins to glucose 6-phosphate via cyclodextrinase (CDase), maltodextrin phosphorylase (Mal-P), and phosphoglucomutase (PGM). These enzymes, which are all induced after growth on starch, were characterized. CGTase catalyzed the conversion of starch to mainly β-cyclodextrin. The gene encoding CGTase was cloned and sequenced and showed highest similarity to a glucanotransferase from Thermococcus litoralis. After transport of the cyclodextrins into the cell by a transport system to be defined, these molecules are linearized via a CDase, catalyzing exclusively the ring opening of the cyclodextrins to the respective maltooligodextrins. These are degraded by a Mal-P to glucose 1-phosphate. Finally, PGM catalyzes the conversion of glucose 1-phosphate to glucose 6-phosphate, which is further degraded to pyruvate via the modified Embden-Meyerhof pathway.