Abiotic versus Biotic Drivers of Ocean pH Variation under Fast Sea Ice in McMurdo Sound,Antarctica

Ocean acidification is expected to have a major effect on the marine carbonate system over the next century, particularly in high latitude seas. Less appreciated is natural environmental variation within these systems, particularly in terms of pH, and how this natural variation may inform laboratory experiments. In this study, we deployed sensor-equipped moorings at 20 m depths at three locations in McMurdo Sound, comprising deep (bottom depth>200 m: Hut Point Peninsula) and shallow environments (bottom depth ∼25 m: Cape Evans and New Harbor). Our sensors recorded high-frequency variation in pH (Hut Point and Cape Evans only), tide (Cape Evans and New Harbor), and water mass properties (temperature and salinity) during spring and early summer 2011. These collective observations showed that (1) pH differed spatially both in terms of mean pH (Cape Evans: 8.009±0.015; Hut Point: 8.020±0.007) and range of pH (Cape Evans: 0.090; Hut Point: 0.036), and (2) pH was not related to the mixing of two water masses, suggesting that the observed pH variation is likely not driven by this abiotic process. Given the large daily fluctuation in pH at Cape Evans, we developed a simple mechanistic model to explore the potential for biotic processes – in this case algal photosynthesis – to increase pH by fixing carbon from the water column. For this model, we incorporated published photosynthetic parameters for the three dominant algal functional groups found at Cape Evans (benthic fleshy red macroalgae, crustose coralline algae, and sea ice algal communities) to estimate oxygen produced/carbon fixed from the water column underneath fast sea ice and the resulting pH change. These results suggest that biotic processes may be a primary driver of pH variation observed under fast sea ice at Cape Evans and potentially at other shallow sites in McMurdo Sound.     

Evaluation of the Phytoextraction Potential at an Acid-Mine-Drainage-Impacted Site

Four plant species were found naturally growing at an acid mine drainage (AMD)-impacted site contaminated with 9430 mg kg^?1Al, 76,000 Fe mg kg^?1, ～150 mg kg^?1Mn, and 420 mg kg^?1 Mg: soybeans (Glycine max), cattails (Typha latifolia), goldenrods (Solidago sp.), and reed grass (Phragmites australis). The metal uptake selectivity was Fe?Mg～Mn>Al for cattails, Mg>Mn>Fe>Al for goldenrods, and Fe?Al>Mg>Mn for reeds. When metal translocation factors, shoot concentrations, and toxicity of the contaminants were correlated, cattails and reeds were more effective at the site than the soybeans or goldenrods. Cattails had a translocation factor of 3.71 for Al, 3.3 for Mg, 1.98 for Mn, and only 0.2 for Fe. The translocation factors for reeds were much higher for Fe (8.64) and Al (7.3). Cattails (1.11 mg Al g^?1 shoot) and reeds (3.4 mg g^?1 g shoot) were both able to hyperaccumulate Al. Additional research is warranted to ascertain if the uptake efficiencies can be enhanced by the use of chelators.     

Effects of Short-Term Climatic Variations on Fluctuating Asymmetry Levels in Chironomus Riparius Larvae at a Polluted Site

We examined fluctuating asymmetry (FA) levels in fourth-instar larvae of Chironomus riparius(Diptera, Chironomidae) collected monthly from a polluted site in Galicia (NW Spain) where pollutant inputs are known to be roughly constant throughout the year. The site was selected because, despite this constancy in pollutant inputs, deformities in fourth-instar larvae were previously found to be more frequent and severe during cold periods and less frequent and severe during warm periods of the year, in accordance with the ‘time-of-exposure’ hypothesis. This hypothesis predicts that short-term climatic variations occurring throughout the year influence the frequency and severity of larval morphological alterations, by means of the control they exert on developmental time and, as a consequence, on the time larvae remain exposed to pollutants. We investigated whether FA levels in larvae were likewise in accordance with this hypothesis, but, contrary to our expectations, no significant differences in FA levels were detected either among months or among seasons, suggesting that FA is not influenced by normal climatic variations. However, climatic influences may be masked, and the observed constancy in FA levels over the sampling period may be a consequence of the action of a mixture of stressors which compensate each other.     

Carbon and Nitrogen Isotopes from Top Predator Amino Acids Reveal Rapidly Shifting Ocean Biochemistry in the Outer California Current

Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS) by measuring δ¹⁵N and δ¹³C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus). Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs) can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰) by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer) δ¹⁵N and δ¹³C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ¹⁵N source-AAs and 3‰ for δ¹³C essential-AAs), while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ¹⁵N and δ¹³C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure.     

Trends in Global Vegetation Activity and Climatic Drivers Indicate a Decoupled Response to Climate Change

Detailed understanding of a possible decoupling between climatic drivers of plant productivity and the response of ecosystems vegetation is required. We compared trends in six NDVI metrics (1982–2010) derived from the GIMMS3g dataset with modelled biomass productivity and assessed uncertainty in trend estimates. Annual total biomass weight (TBW) was calculated with the LINPAC model. Trends were determined using a simple linear regression, a Thiel-Sen medium slope and a piecewise regression (PWR) with two segments. Values of NDVI metrics were related to Net Primary Production (MODIS-NPP) and TBW per biome and land-use type. The simple linear and Thiel-Sen trends did not differ much whereas PWR increased the fraction of explained variation, depending on the NDVI metric considered. A positive trend in TBW indicating more favorable climatic conditions was found for 24% of pixels on land, and for 5% a negative trend. A decoupled trend, indicating positive TBW trends and monotonic negative or segmented and negative NDVI trends, was observed for 17–36% of all productive areas depending on the NDVI metric used. For only 1–2% of all pixels in productive areas, a diverging and greening trend was found despite a strong negative trend in TBW. The choice of NDVI metric used strongly affected outcomes on regional scales and differences in the fraction of explained variation in MODIS-NPP between biomes were large, and a combination of NDVI metrics is recommended for global studies. We have found an increasing difference between trends in climatic drivers and observed NDVI for large parts of the globe. Our findings suggest that future scenarios must consider impacts of constraints on plant growth such as extremes in weather and nutrient availability to predict changes in NPP and CO₂ sequestration capacity.     

In Vivo Intracellular pH Measurements in Tobacco and Arabidopsis Reveal an Unexpected pH Gradient in the Endomembrane System

The pH homeostasis of endomembranes is essential for cellular functions. In order to provide direct pH measurements in the endomembrane system lumen, we targeted genetically encoded ratiometric pH sensors to the cytosol, the endoplasmic reticulum, and the trans-Golgi, or the compartments labeled by the vacuolar sorting receptor (VSR), which includes the trans-Golgi network and prevacuoles. Using noninvasive live-cell imaging to measure pH, we show that a gradual acidification from the endoplasmic reticulum to the lytic vacuole exists, in both tobacco (Nicotiana tabacum) epidermal (ΔpH −1.5) and Arabidopsis thaliana root cells (ΔpH −2.1). The average pH in VSR compartments was intermediate between that of the trans-Golgi and the vacuole. Combining pH measurements with in vivo colocalization experiments, we found that the trans-Golgi network had an acidic pH of 6.1, while the prevacuole and late prevacuole were both more alkaline, with pH of 6.6 and 7.1, respectively. We also showed that endosomal pH, and subsequently vacuolar trafficking of soluble proteins, requires both vacuolar-type H⁺ ATPase–dependent acidification as well as proton efflux mediated at least by the activity of endosomal sodium/proton NHX-type antiporters.     

Modeling Soil and Biomass Carbon Responses to Declining Water Table in a Wetland-Rich Landscape

Peatlands and forested wetlands can cover a large fraction of the land area and contain a majority of the regional carbon pool in wet northern temperate landscapes. We used the LANDIS-II forest landscape succession model coupled with a model of plant community and soil carbon responses to water table changes to explore the impacts of declining water table on regional carbon pools in a peatland- and wetland-rich landscape in northern Wisconsin, USA. Simulations indicated that both biomass accumulation and soil decomposition would increase as a consequence of drying. In peatlands, simulated water table declines of 100 cm led to large increases in biomass as well as short-term increases in soil carbon, whereas declines of 40 cm led to continuous declines in soil carbon and smaller increases in biomass, with the net result being a loss of total carbon. In non-peat wetlands, biomass accumulation outweighed soil carbon loss for both scenarios. Long-term carbon cycle responses were not significantly affected by the time scale of water table decline. In general, peatland carbon storage over the first 50–150 years following drainage was neutral or increasing due to increased plant growth, whereas carbon storage over longer time scales decreased due to soil carbon loss. Although the simplicity of the model limits quantitative interpretation, the results show that plant community responses are essential to understanding the full impact of hydrological change on carbon storage in peatland-rich landscapes, and that measurements over long time scales are necessary to adequately constrain landscape carbon pool responses to declining water table.     

Quantifying Geographic Variation in the Climatic Drivers of Midcontinent Wetlands with a Spatially Varying Coefficient Model

The wetlands in the Prairie Pothole Region and in the Great Plains are notorious for their sensitivity to weather variability. These wetlands have been the focus of considerable attention because of their ecological importance and because of the expected impact of climate change. Few models in the literature, however, take into account spatial variation in the importance of wetland drivers. This is surprising given the importance spatial heterogeneity in geomorphology and climatic conditions have in the region. In this paper, I use spatially-varying coefficients to assess the variation in ecological drivers in a number of ponds observed over a 50-year period (1961-2012). I included the number of ponds observed the year before on a log scale, the log of total precipitation, and mean maximum temperature during the four previous seasons as explanatory variables. I also included a temporal component to capture change in the number of ponds due to anthropogenic disturbance. Overall, fall and spring precipitation were most important in pond abundance in the west, whereas winter and summer precipitation were the most important drivers in the east. The ponds in the east of the survey area were also more dependent on pond abundance during the previous year than those in the west. Spring temperature during the previous season influenced pond abundance; while the temperature during the other seasons had a limited effect. The ponds in the southwestern part of the survey area have been increasing independently of climatic conditions, whereas the ponds in the northeast have been steadily declining. My results underline the importance of accounting the spatial heterogeneity in environmental drivers, when working at large spatial scales. In light of my results, I also argue that assessing the impacts of climate change on wetland abundance in the spring, without more accurate climatic forecasting, will be difficult.     

Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei

Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 10⁵ to 6.6 × 10⁶ cells m⁻³ of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.Microbes are abundant in the atmosphere, with both cultivation-dependent and molecular approaches showing that the atmosphere harbors a diverse assemblage of bacteria and fungi, including taxa also commonly found on leaf surfaces (5, 49) and in soil habitats (30). The abundance and composition of airborne microbial communities are variable across time and space (14, 24, 27, 33, 47, 48, 69). However, the atmospheric conditions responsible for driving the observed changes in microbial abundances are unknown. The diversity of airborne microorganisms, and the factors influencing diversity levels, also remains poorly characterized. One reason for these limitations in knowledge is that until recently, culture-based microbiological methods have been the standard, and it is well-recognized that such methods capture only a small portion of the total microbial diversity (59). As demonstrated in a number of recent studies (6, 13, 22, 23, 33, 52, 59, 63, 73), advances in culture-independent techniques allow far more of the microbial diversity present in the atmosphere to be surveyed and the spatiotemporal variability in microbial communities to be examined.Microbes are often considered passive inhabitants of the atmosphere, dispersing via airborne dust particles. However, recent studies suggest that many atmospheric microbes may be metabolically active (3, 4, 64), even up to altitudes of 20,000 m (34). Some airborne microbes may alter atmospheric conditions directly by acting as cloud condensation nuclei (7, 25, 56) and/or ice nuclei (IN) (19, 41, 56, 57, 61); this hypothesis is supported by the observation that most ice nuclei in snow samples are inactivated by a 95°C heat treatment (16, 17). However, the overall contribution of airborne microbes to atmospheric processes such as ice nucleation remains unclear.The best-studied ice-nucleating microbes are gram-negative bacteria that have also been isolated from leaf surfaces, including Pseudomonas syringae, Pseudomonas fluorescens, Erwinia herbicola, Xanthomonas campestri, and Sphingomonas spp. (45). These bacteria have been cultured extensively, and their ice-nucleating activity has been traced to a membrane-bound glycoprotein (40, 42, 70). However, their specific influence on atmospheric processes remains, at this point, largely anecdotal. Less is known about the ice-nucleating activities of fungi, but a few studies have shown that fungi can be effective ice nucleators, capable of initiating ice nucleation at temperatures as high as −2°C (41, 61). At this point, all known ice-nucleating microorganisms are amenable to culture-based studies, but given that the vast majority of microorganisms have yet to be cultured, it is likely that other ice-nucleating microbes remain undiscovered.The work presented here addresses three overarching questions. (i) Are microbial abundances altered by changes in atmospheric conditions? (ii) How is the diversity and composition of airborne microbial communities influenced by changes in atmospheric conditions? (iii) Can we identify known and novel ice-nucleating microbes in the atmosphere by testing for correlations between taxa abundances and the concentrations of biological ice nuclei? To address these questions, we combined epifluorescence microscopy, tagged pyrosequencing, Sanger sequencing, and an ice nucleation assay with atmospheric measurements to characterize the microbial communities at a high-elevation research site.     

T Cells at the Site of Autoimmune Inflammation Show Increased Potential for Trogocytosis

CD4+ T cells acquire membrane fragments from antigen-presenting-cells via a process termed trogocytosis. Identifying which CD4+ T cells undergo trogocytosis in co-culture with Ag-loaded APC can enrich for antigen-reactive T cells without knowledge of their fine specificity or cytokine-production profiles. We sought to assess the suitability of this method to identify disease relevant effector and regulatory T cells during autoimmune inflammation. Trogocytosis efficiently identified MBP-reactive T cells in vitro and ex-vivo following immunization. However, Foxp3+ regulatory T cells constitutively displayed a higher rate of trogocytosis than their Foxp3- counterparts which limits the potential of trogocytosis to identify antigen-reactive Treg cells. During inflammation a locally elevated rate of trogocytosis (seen in both effector and regulatory T cells isolated from the inflamed CNS) precludes the use of trogocytosis as a measure of antigenic reactivity among cells taken from inflammatory sites. Our results indicate trogocytosis detection can enrich for Ag-reactive conventional T cells in the periphery but is limited in its ability to identify Ag-reactive Treg or T effector cells at sites of inflammation. Increased trogocytosis potential at inflammatory sites also draws into the question the biological significance of this phenomenon during inflammation, in Treg mediated suppression and for the maintenance of tolerance in health and disease.     

pH Measurements of Agar Culture Media by Using a Flat-Bottom Electrode

A new design, flat-bottom combination pH electrode was evaluated for utility in determining the pH of prepared agar media by surface contact of the electrode with the agar media.     

Agricultural Management and Climatic Change Are the Major Drivers of Biodiversity Change in the UK

Action to reduce anthropogenic impact on the environment and species within it will be most effective when targeted towards activities that have the greatest impact on biodiversity. To do this effectively we need to better understand the relative importance of different activities and how they drive changes in species’ populations. Here, we present a novel, flexible framework that reviews evidence for the relative importance of these drivers of change and uses it to explain recent alterations in species’ populations. We review drivers of change across four hundred species sampled from a broad range of taxonomic groups in the UK. We found that species’ population change (~1970–2012) has been most strongly impacted by intensive management of agricultural land and by climatic change. The impact of the former was primarily deleterious, whereas the impact of climatic change to date has been more mixed. Findings were similar across the three major taxonomic groups assessed (insects, vascular plants and vertebrates). In general, the way a habitat was managed had a greater impact than changes in its extent, which accords with the relatively small changes in the areas occupied by different habitats during our study period, compared to substantial changes in habitat management. Of the drivers classified as conservation measures, low-intensity management of agricultural land and habitat creation had the greatest impact. Our framework could be used to assess the relative importance of drivers at a range of scales to better inform our policy and management decisions. Furthermore, by scoring the quality of evidence, this framework helps us identify research gaps and needs.     

Molecular Structure and Regulatory Potential of a T-DNA Integration Site in Petunia

The genomic structure surrounding a T-DNA integration site in a transgenic petunia plant, which shows deregulation of a root-specific promoter, was investigated. We have already demonstrated that T-DNA integration in this transformant (P13) had occurred close to a scaffold/matrix attachment region (S/MAR). A major question regarding the observed promoter leakiness was whether the T-DNA had integrated into the centre or at the border of the Petun-SAR and whether other regulatory elements are located within this genomic region. While small rearrangements were shown to occur during T-DNA integration in agreement with other reports, we find indications of the presence of a SINE retroposon – an apparent landmark for recombinogenic targets – at the integration site. Binding assays to both plant and animal nuclear scaffolds, supported by biomathematical analyses, reveal that the T-DNA is definitely located at the border of a strong S/MAR, which is in agreement with current models on the structure of integration sites. These results, together with a developmentally regulated leaf-specific enhancer effect of the Petun-SAR on gene expression in transgenic tobacco plants, indicate that the Petun-SAR demarcates the right border of a chromatin domain with genes predominantly active in leaves.     

O-糖基化位点预测及糖基化酶催化特点

O-糖链维持所连接蛋白质部分的空间构象。O-糖基化作为生物体内重要的生物过程,其起始步骤具有复杂的高度选择性,迄今为止还未发现固定的模式。人们通过比较已知O-糖基化部位周围的氨基酸序列,推测出O-糖基化位点的一些规律及其酶的催化特性。     

Biotic and Abiotic Drivers of Topsoil Organic Carbon Concentration in Drylands Have Similar Effects at Regional and Global Scales

Ecosystems - Drylands contain 25% of the world’s soil organic carbon (SOC), which is controlled by many factors, both abiotic and biotic. Thus, understanding how these factors control SOC...     

Carbon monoxide complex of cytochrome b(5) at acidic pH

CO complex of cyt b(5) generated at acidic pH is investigated by absorption, resonance Raman (RR), and far UV CD measurements. The Soret maximum wavelength blue-shifted to 420 nm with other absorption bands observed around 540 and 570 nm for reduced cyt b(5) upon interaction with CO at acidic pH (pH 3.1-3.5). Under this condition, the iron-carbon stretching RR band was observed at 529 cm(-1) (520 cm(-1) for C(18)O), which indicated formation of a heme&bond;CO adduct with a histidine as an axial ligand. Heme dissociated from the reduced cyt b(5) protein at pH approximately 3.5, whereas its rate decreased under CO atmosphere compared with N(2) atmosphere, due to formation of a heme&bond;CO adduct with a histidine as an axial ligand.     

Assessing the Potential of Phytoremediation at a Site in the U.K. Contaminated With 137Cs

Spinacia oleracea L. cv. ‘Bloomsdale’, Beta vulgaris L. cv. ‘Flavescens’, Brassica juncea L. ‘OB825’, and Helianthus annuus L. cv. ‘Oranges and Lemons’ were grown for 8 weeks at a site contaminated with ¹³⁷Cs at Bradwell Nuclear Power Station, UK. The site was a trench approximately 1.5 m deep, 2 m wide, and 100 m long in ‘made ground’ consisting of alluvium with traces of illites, kaolinites, and smectites. ¹³⁷Cs activity concentration was measured in individual plants after 8 weeks growth and the soil in which they grew. The biomass produced and total ¹³⁷Cs removed to shoots differed significantly between species but ¹³⁷Cs activity concentrations and Transfer Factors (TFs) did not. B. vulgaris produced the most biomass and removed the greatest amount of ¹³⁷Cs. For all plants, and within each taxon, plants growing at low soil ¹³⁷Cs activity concentrations had significantly greater TFs than those growing at high soil ¹³⁷Cs activity concentrations. It is concluded that selecting plant taxa suited to a particular site can be an effective way of improving phytoremediation rates, that there is much scope for adjusting harvesting intervals to 8 weeks or less without affecting TFs, and that estimates of time taken for ¹³⁷Cs removal by phytoremediation should consider that TFs may increase as soil concentrations decrease. With refinements in methodology, phytoremediation has the potential to contribute significantly to decontamination of the site at Bradwell.