High bicarbonate assimilation in the dark by Arctic bacteria

10 páginas, 4 figuras, 1 tabla.Although both autotrophic and heterotrophic microorganisms incorporate CO2 in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. We studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter Arctic seawater. At stationary phase, bicarbonate incorporation rates were high (0.5–2.5 μg C L−1 d−1) and correlated with rates of bacterial heterotrophic production, suggesting that most of the incorporation was due to heterotrophs. Accordingly, very few typically chemoautotrophic bacteria were detected by 16S rRNA gene cloning. The genetic analysis of the biotin carboxylase gene accC putatively involved in archaeal CO2 fixation did not yield any archaeal sequence, but amplified a variety of bacterial carboxylases involved in fatty acids biosynthesis, anaplerotic pathways and leucine catabolism. Gammaproteobacteria dominated the seawater cultures (40–70% of cell counts), followed by Betaproteobacteria and Flavobacteria as shown by catalyzed reporter deposition fluorescence in situ hybridization (CARDFISH). Both Beta- and Gammaproteobacteria were active in leucine and bicarbonate uptake, while Flavobacteria did not take up bicarbonate, as measured by microautoradiography combined with CARDFISH. Within Gammaproteobacteria, Pseudoalteromonas-Colwellia and Oleispira were very active in bicarbonate uptake (ca. 30 and 70% of active cells, respectively), while the group Arctic96B-16 did not take up bicarbonate. Our results suggest that, potentially, the incorporation of CO2 can be relevant for the metabolism of specific Arctic heterotrophic phylotypes, promoting the maintenance of their cell activity and/or longer survival under resource depleted conditions.This work is a contribution to the International Polar Year – Circumpolar Flaw Lead system study (IPY-CFL 2007/2008) lead by D. Barber (University of Manitoba) supported through grants from the Canadian IPY Federal Program Office, the National Sciences and Engineering Research Council, grant BOREAL (CLG2007-28872-E/ANT) from the Spanish Ministry of Science and Innovation to C.P.-A., and grants from the Swedish Research Council to S.B and L.A.S. L.A.S. was supported by a Marie Curie Intraeuropean Fellowship (CHEMOARC PIEF-GA-2008- 221121), E.O.C by the Spanish grant CGL2009-13318- BOS, and P. E. G by a Marie Curie grant (CRENARC MEIF-CT-2007-040247).Peer reviewe

The Amundsen Sea Polynya International Research Expedition (ASPIRE)

In search of an explanation for some of the greenest waters ever seen in coastal Antarctica and their possible link to some of the fastest melting glaciers and declining summer sea ice, the Amundsen Sea Polynya International Research Expedition (ASPIRE) challenged the capabilities of the US Antarctic Program and RVIB Nathaniel B. Palmer during Austral summer 2010–2011. We were well rewarded by both an extraordinary research platform and a truly remarkable oceanic setting. Here we provide further insights into the key questions that motivated our sampling approach during ASPIRE and present some preliminary findings, while highlighting the value of the Palmer for accomplishing complex, multifaceted oceanographic research in such a challenging environment

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera "Candidatus Planktophila" (acI-A) and "Candidatus Nanopelagicus" (acI-B) and the proteobacterial genus "Candidatus Fonsibacter" (LD12). While "Ca. Planktophila" and "Ca. Fonsibacter" had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which "Ca. Planktophila" is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain "Ca. Planktophila" population abundance, the success of "Ca. Nanopelagicus" and "Ca. Fonsibacter" is better explained as a community by-product. Ecotype differentiation of "Ca. Fonsibacter" as a means of escaping predation was supported but not for overcoming auxotrophies.IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: "Ca. Planktophila" (acI-A), "Ca. Nanopelagicus" (acI-B), and "Ca. Fonsibacter" (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied

Summer comes to the Southern Ocean: how phytoplankton shape bacterioplankton communities far into the deep dark sea

18 pages, 6 figures, 1 table, supporting information https://doi.org/10.1002/ecs2.2641During austral spring and summer, the coastal Antarctic experiences a sharp increase in primary production and a steepening of biotic and abiotic gradients that result from increased solar radiation and retreating sea ice. In one of the largest seasonally ice-free regions, the Amundsen Sea Polynya, pelagic samples were collected from 15 sites during a massive Phaeocystis antarctica bloom in 2010/2011. Along with a suite of other biotic and abiotic measurements, bacterioplankton were collected and analyzed for community structure by pyrosequencing of the 16S rRNA gene. The aims were to identify patterns in diversity and composition of heterotrophic bacterioplankton and to test mechanistic hypotheses for explaining these differences along variations in depth, water mass, phytoplankton biomass, and organic and inorganic nutrients. The overall goal was to clarify the relationship between primary producers and bacterioplankton community structure in the Southern Ocean. Results suggested that both epipelagic and mesopelagic bacterioplankton communities were structured by phytoplankton blooming in the euphotic zone. As chlorophyll a (chl-a) increased in surface waters, the abundance of surface bacterioplankton increased, but their diversity decreased. Similarity in bacterioplankton community composition between surface-water sites increased as the bloom progressed, suggesting that algal blooms may homogenize surface-water bacterioplankton communities at larger spatial scales. Below the euphotic zone, the opposite relationship was found. Mesopelagic bacterioplankton diversity increased with increasing chl-a in the overlying surface waters. This shift may be promoted by several factors including local increase in organic and inorganic nutrients from particles sinking out of the euphotic zone, an increase in niche differentiation associated with the particle flux, interactions with deep-dwelling macrozooplankton, and release from competition with primary producers. Additional multivariate analyses of bacterioplankton community structure and nutrient concentrations revealed distinct depth horizons, with bacterioplankton communities having maximum alpha and beta diversity just below the euphotic zone, while nutrient composition gradually homogenized with increasing depth. Our results provide evidence for bloom-driven (bottom-up) control of bacterioplankton community diversity in the coastal Southern Ocean and suggest mechanisms whereby surface processes can shape the diversity of bacterioplankton communities at great depthThe study was funded by the Swedish Research Council (grants to SB and LR) and the U.S. National Science Foundation through the ASPIRE project (ANT‐0839069

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum

Controls on the composition and lability of dissolved organic matter in Siberia's Kolyma River basin

High-latitude northern rivers export globally significant quantities of dissolved organic carbon (DOC) to the Arctic Ocean. Climate change, and its associated impacts on hydrology and potential mobilization of ancient organic matter from permafrost, is likely to modify the flux, composition, and thus biogeochemical cycling and fate of exported DOC in the Arctic. This study examined DOC concentration and the composition of dissolved organic matter (DOM) across the hydrograph in Siberia's Kolyma River, with a particular focus on the spring freshet period when the majority of the annual DOC load is exported. The composition of DOM within the Kolyma basin was characterized using absorbance-derived measurements (absorbance coefficienta330, specific UV absorbance (SUVA254), and spectral slope ratio SR) and fluorescence spectroscopy (fluorescence index and excitation-emission matrices (EEMs)), including parallel factor analyses of EEMs. Increased surface runoff during the spring freshet led to DOM optical properties indicative of terrestrial soil inputs with high humic-like fluorescence, SUVA254, and low SRand fluorescence index (FI). Under-ice waters, in contrast, displayed opposing trends in optical properties representing less aromatic, lower molecular weight DOM. We demonstrate that substantial losses of DOC can occur via biological (∼30% over 28 days) and photochemical pathways (>29% over 14 days), particularly in samples collected during the spring freshet. The emerging view is therefore that of a more dynamic and labile carbon pool than previously thought, where DOM composition plays a fundamental role in controlling the fate and removal of DOC at a pan-Arctic scale

Importance of Ethnicity, CYP2B6 and ABCB1 Genotype for Efavirenz Pharmacokinetics and Treatment Outcomes: A Parallel-group Prospective Cohort Study in two sub-Saharan Africa Populations.

We evaluated the importance of ethnicity and pharmacogenetic variations in determining efavirenz pharmacokinetics, auto-induction and immunological outcomes in two African populations. ART naïve HIV patients from Ethiopia (n = 285) and Tanzania (n = 209) were prospectively enrolled in parallel to start efavirenz based HAART. CD4+ cell counts were determined at baseline, 12, 24 and 48 weeks. Plasma and intracellular efavirenz and 8-hydroxyefvairenz concentrations were determined at week 4 and 16. Genotyping for common functional CYP2B6, CYP3A5, ABCB1, UGT2B7 and SLCO1B1 variant alleles were done. Patient country, CYP2B6*6 and ABCB1 c.4036A>G (rs3842A>G) genotype were significant predictors of plasma and intracellular efavirenz concentration. CYP2B6*6 and ABCB1 c.4036A>G (rs3842) genotype were significantly associated with higher plasma efavirenz concentration and their allele frequencies were significantly higher in Tanzanians than Ethiopians. Tanzanians displayed significantly higher efavirenz plasma concentration at week 4 (p<0.0002) and week 16 (p = 0.006) compared to Ethiopians. Efavirenz plasma concentrations remained significantly higher in Tanzanians even after controlling for the effect of CYP2B6*6 and ABCB1 c.4036A>G genotype. Within country analyses indicated a significant decrease in the mean plasma efavirenz concentration by week 16 compared to week 4 in Tanzanians (p = 0.006), whereas no significant differences in plasma concentration over time was observed in Ethiopians (p = 0.84). Intracellular efavirenz concentration and patient country were significant predictors of CD4 gain during HAART. We report substantial differences in efavirenz pharmacokinetics, extent of auto-induction and immunologic recovery between Ethiopian and Tanzanian HIV patients, partly but not solely, due to pharmacogenetic variations. The observed inter-ethnic variations in efavirenz plasma exposure may possibly result in varying clinical treatment outcome or adverse event profiles between populations

Real-time Accelerator Diagnostic Tools for the MAX IV Storage Rings

In this paper, beam diagnostic and monitoring tools developed by the MAX IV Operations Group are discussed. In particular, new beam position monitoring and accelerator tunes visualization software tools, as well as tools that directly influence the beam quality and stability are introduced. An availability and downtime monitoring application is also presented

Sustainability marketing myopia: the lack of sustainability communication persuasiveness

Sustainability communication in accommodation businesses tends to be factual and descriptive, as companies are concerned with product-based messages that focus on what they do; they appear not to understand the potential benefits of constructing messages that would influence consumers to behave more sustainably, which is effectively sustainability marketing myopia. An analysis of 1,835 sustainability messages from award-winning businesses shows that messages communicate facts not emotions, and benefits for society as a whole rather than for the individual customer. The messages are explicit, but passive and not experiential hence they positively affect the cognitive but not the affective image of the business. The lack of message normalization and customer focus reinforces the image of sustainability being a niche concern. We reflect on the reasons for these shortcomings and highlight opportunities to improve persuasive communication, which we have now applied commercially in more than 400 website analyses and 60 training courses