Inorganic carbon and nitrogen assimilation in cellular compartments of a benthic kleptoplastic foraminifer

© The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 10140, doi:10.1038/s41598-018-28455-1.Haynesina germanica, an ubiquitous benthic foraminifer in intertidal mudflats, has the remarkable ability to isolate, sequester, and use chloroplasts from microalgae. The photosynthetic functionality of these kleptoplasts has been demonstrated by measuring photosystem II quantum efficiency and O2 production rates, but the precise role of the kleptoplasts in foraminiferal metabolism is poorly understood. Thus, the mechanism and dynamics of C and N assimilation and translocation from the kleptoplasts to the foraminiferal host requires study. The objective of this study was to investigate, using correlated TEM and NanoSIMS imaging, the assimilation of inorganic C and N (here ammonium, NH4+) in individuals of a kleptoplastic benthic foraminiferal species. H. germanica specimens were incubated for 20 h in artificial seawater enriched with H13CO3− and 15NH4+ during a light/dark cycle. All specimens (n = 12) incorporated 13C into their endoplasm stored primarily in the form of lipid droplets. A control incubation in darkness resulted in no 13C-uptake, strongly suggesting that photosynthesis is the process dominating inorganic C assimilation. Ammonium assimilation was observed both with and without light, with diffuse 15N-enrichment throughout the cytoplasm and distinct 15N-hotspots in fibrillar vesicles, electron-opaque bodies, tubulin paracrystals, bacterial associates, and, rarely and at moderate levels, in kleptoplasts. The latter observation might indicate that the kleptoplasts are involved in N assimilation. However, the higher N assimilation observed in the foraminiferal endoplasm incubated without light suggests that another cytoplasmic pathway is dominant, at least in darkness. This study clearly shows the advantage provided by the kleptoplasts as an additional source of carbon and provides observations of ammonium uptake by the foraminiferal cell.This work was supported by the Swiss National Science Foundation (grant no. 200021_149333) and was part of the CNRS EC2CO-Lefe project ForChlo. It was also supported by the Region Pays de la Loire (Post-doc position of TJ, on FRESCO project) as well as the WHOI Robert W. Morse Chair for Excellence in Oceanography and The Investment in Science Fund at WHOI

Ultrastructure and distribution of kleptoplasts in benthic foraminifera from shallow-water (photic) habitats

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Micropaleontology 138 (2018): 46-62, doi:10.1016/j.marmicro.2017.10.003.Assimilation, sequestration and maintenance of foreign chloroplasts inside an organism is termed “chloroplast sequestration” or “kleptoplasty”. This phenomenon is known in certain benthic foraminifera, in which such kleptoplasts can be found both intact and functional, but with different retention times depending on foraminiferal species. In the present study, seven species of benthic foraminifera (Haynesina germanica, Elphidium williamsoni, E. selseyense, E. oceanense, E. aff. E. crispum, Planoglabratella opercularis and Ammonia sp.) were collected from shallow-water benthic habitats and examined with transmission electron microscope (TEM) for cellular ultrastructure to ascertain attributes of kleptoplasts. Results indicate that all these foraminiferal taxa actively obtain kleptoplasts but organized them differently within their endoplasm. In some species, the kleptoplasts were evenly distributed throughout the endoplasm (e.g., H. germanica, E. oceanense, Ammonia sp.), whereas other species consistently had plastids distributed close to the external cell membrane (e.g., Elphidium williamsoni, E. selseyense, P. opercularis). Chloroplast degradation also seemed to differ between species, as many degraded plastids were found in Ammonia sp. and E. oceanense compared to other investigated species. Digestion ability, along with different feeding and sequestration strategies may explain the differences in retention time between taxa. Additionally, the organization of the sequestered plastids within the endoplasm may also suggest behavioral strategies to expose and/or protect the sequestered plastids to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats.TJ was funded by the “FRESCO” project, a project supported by the Region Pays de Loire and the University of Angers. This work was also supported by a grant no. 200021_149333 from the Swiss National Science Foundation and the French national program EC2CO-LEFE (project ForChlo).JMB acknowledges the Robert W. Morse Chair for Excellence in Oceanography and the Investment in Science Fund at WHOI. Also, KK acknowledges the Academy of Finland (Project numbers: 278827, 283453)

Experimental fossilisation of viruses from extremophilic Archaea

The role of viruses at different stages of the origin of life has recently been reconsidered. It appears that viruses may have accompanied the earliest forms of life, allowing the transition from an RNA to a DNA world and possibly being involved in the shaping of tree of life in the three domains that we know presently. In addition, a large variety of viruses has been recently identified in extreme environments, hosted by extremophilic microorganisms, in ecosystems considered as analogues to those of the early Earth. Traces of life on the early Earth were preserved by the precipitation of silica on the organic structures. We present the results of the first experimental fossilisation by silica of viruses from extremophilic Archaea (SIRV2 – <i>Sulfolobus islandicus</i> rod-shaped virus 2, TPV1 – <i>Thermococcus prieurii</i> virus 1, and PAV1 – <i>Pyrococcus abyssi</i> virus 1). Our results confirm that viruses can be fossilised, with silica precipitating on the different viral structures (proteins, envelope) over several months in a manner similar to that of other experimentally and naturally fossilised microorganisms. This study thus suggests that viral remains or traces could be preserved in the rock record although their identification may be challenging due to the small size of the viral particles

The State of the World’s Urban Ecosystems: what can we learn from trees, fungi and bees?

Trees are a foundation for biodiversity in urban ecosystems and therefore must be able to withstand global change and biological challenges over decades and even centuries to prevent urban ecosystems from deteriorating. Tree quality and diversity should be prioritized over simply numbers to optimize resilience to these challenges. Successful establishment and renewal of trees in cities must also consider belowground (e.g., mycorrhizas) and aboveground (e.g., pollinators) interactions to ensure urban ecosystem longevity, biodiversity conservation and continued provision of the full range of ecosystem services provided by trees. Positive interactions with nature inspire people to live more sustainable lifestyles that are consistent with stopping biodiversity loss and to participate in conservation actions such as tree‐planting and supporting pollinators. Interacting with nature simultaneously provides mental and physical health benefits to people. Since most people live in cities, here we argue that urban ecosystems provide important opportunities for increasing engagement with nature and educating people about biodiversity conservation. While advocacy on biodiversity must communicate in language that is relevant to a diverse audience, over‐simplified messaging, may result in unintended negative outcomes. For example, tree planting actions typically focus on numbers rather than diversity while the call to save bees has inspired unsustainable proliferation of urban beekeeping that may damage wild bee conservation through increased competition for limited forage in cities and disease spread. Ultimately multiple ecosystem services must be considered (and measured) to optimize their delivery in urban ecosystems and messaging to promote the value of nature in cities must be made widely available and more clearly defined

MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms

Background: The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results: We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions: The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea as well as eukaryotic organisms. This success rate compares favorably with other protein screening projects, particularly for eukaryotic proteins. Several purified targets have already formed the base for experiments aimed at post-genomic validation

Foraminiferal species responses to in situ, experimentally induced anoxia in the Adriatic Sea

Anoxia was successfully induced in four benthic chambers installed at 24 m depth in the northern Adriatic Sea for periods varying from 9 days to 10 months. During the 10-month period, species richness significantly decreased. Although no significant change in Shannon diversity and evenness was observed, the composition of the foraminiferal assemblages changed with time. This change is due to interspecific differences in tolerance to anoxia. Reophax nanus, Textularia agglutinans and Quinqueloculina stelligera all showed a significant decrease with time, strongly suggesting they are sensitive to anoxia. Conversely, Eggerella scabra, Bulimina marginata, Lagenammina atlantica, Hopkinsina pacifica and Bolivina pseudoplicata appeared to be resistant to the experimental conditions. Quinqueloculina seminula was apparently sensitive to anoxia but showed a clear standing stock increase during the first month of the experiment, which we interpret as an opportunistic response to increasing organic matter availability due to the degradation of the dead macrofaunal organisms. None of the anoxia-sensitive species is able to accumulate intracellular nitrates. Nitrate accumulation could be shown for some tested specimens of the dominant anoxia-tolerant species E. scabra and B. marginata. However, tests on the denitrification capacity of these taxa yielded negative results, suggesting that their resistance to long-term anoxia is not due to their ability to denitrify

Foraminiferal survival after long-term in situ experimentally induced anoxia

Anoxia was successfully induced in four benthic chambers installed at 24 m depth on the northern Adriatic seafloor from 9 days to 10 months. To accurately determine whether benthic foraminifera can survive experimentally induced prolonged anoxia, the CellTrackerTM Green method was applied and calcareous and agglutinated foraminifera were analyzed. Numerous individuals were found living at all sampling times and at all sampling depths (to 5 cm), supported by a ribosomal RNA analysis that revealed that certain benthic foraminifera were active after 10 months of anoxia. The results show that benthic foraminifera can survive up to 10 months of anoxia with co-occurring hydrogen sulfides. However, foraminiferal standing stocks decrease with sampling time in an irregular manner. A large difference in standing stock between two cores sampled under initial conditions indicates the presence of a large spatial heterogeneity of the foraminiferal faunas. An unexpected increase in standing stocks after one month is tentatively interpreted as a reaction to increased food availability due to the massive mortality of infaunal macrofaunal organisms. After this, standing stocks decrease again in cores sampled after 2 months of anoxia to then attain a minimum in the cores sampled after 10 months. We speculate that the trend of overall decrease of standing stocks is not due to the adverse effects of anoxia and hydrogen sulfides but rather due to a continuous diminution of labile organic matter

Evaluating Niger's experience in strengthening supervision, improving availability of child survival drugs through cost recovery, and initiating training for Integrated Management of Childhood Illness (IMCI)

BACKGROUND: WHO and UNICEF have recently developed the "Integrated Management of Childhood Illness" (IMCI) as an efficient strategy to assist developing countries reduce childhood mortality. Early experience with IMCI implementation suggests that clinical training is essential but not sufficient for the success of the strategy. Attention needs to be given to strengthening health systems, such as supervision and drug supply. RESULTS: This paper presents results of evaluating an innovative approach for implementing IMCI in Niger. It starts with strengthening district level supervision and improving the availability of child survival drugs through cost recovery well before the beginning of IMCI clinical training. The evaluation documented the effectiveness of the initial IMCI clinical training and referral. CONCLUSIONS: Strengthening supervision and assuring the availability of essential drugs need to precede the initiation of IMCI Clinical training. Longer term follow up is necessary to confirm the impact of the approach on IMCI preparation and implementation

Contribution de la culture des foraminifères benthiques à la calibration de proxies paléocéanographiques

Grâce aux connaissances acquises sur les conditions idéales de culture de différentes espèces de foraminifères benthiques, il est désormais possible de réaliser des calibrations de proxies paléocéanographiques en laboratoire. Plusieurs expériences ont déjà été réalisées : 1) Calibration du δ18O de foraminifères benthiques profonds (Barras et al., 2010) La culture de Bulimina marginata en conditions contrôlées à différentes températures (4 à 19°C) a permis de démontrer que l’effet de la température sur le δ18O de cette espèce est semblable à l’effet thermodynamique enregistré pour la calcite inorganique. Nous avons pu mettre en évidence également un effet ontogénétique non négligeable pour les études de reconstitutions paléoclimatiques. 2) Calibration du Mg/Ca de coquilles de Hyalinea balthica (Rosenthal et al., 2011) La calcification de nouvelles loges de H. balthica à différentes températures (8, 10 et 13°C) a permis de mesurer, à l’aide de l’ablation laser ICP-MS, un effet d’environ 12%/°C sur la concentration en Mg/Ca. Ces résultats confirment la calibration in situ réalisée pour cette espèce qui se trouve avoir une sensibilité 4 fois supérieure à celle des autres espèces benthiques profondes. 3) Effet de la salinité sur le δ18O, le Mg/Ca et le Sr/Ca d’une espèce côtière (Diz et al., 2012) La culture d’Ammonia tepida en conditions contrôlées à différentes salinités (29.8, 32.2, 35.5) n’a pas montré d’effet significatif de ce paramètre sur la composition isotopique et en éléments traces de la calcite. Par contre, ces expériences ont permis de mettre en évidence un effet de la taille des individus sur la composition en Sr/Ca et une forte variabilité des mesures de Mg/Ca entre les coquilles d’individus ayant calcifié dans les mêmes conditions. 4) Effet de la nourriture sur le δ13C d’espèces intertidales (Mojtahid et al., 2011) Des expériences menées en laboratoire sur des coquilles adultes de Hyanesina germanica et A. beccarii avec de la nourriture labélisée radioactivement (3H et 14C) ont montré que très peu de carbone ingéré est incorporé dans la coquille. Cependant, aucun des spécimens n’a formé de nouvelles loges pendant les expériences ce qui ne permet pas une conclusion définitive sur l’influence de la nourriture sur la signature isotopique de la calcite. Ceci ouvre les portes à d’autres expériences sur des juvéniles avec le même protocole qui s’est avéré très approprié. Ces études ont démontré l’utilité de réaliser des calibrations de proxies en laboratoire. Nous prévoyons de poursuivre ce travail en travaillant au développement de nouveaux proxies de paléo-oxygénation grâce au programme de recherche régional MADONA

Double-J ureteral stent under local anesthesia for women

INTRODUCTION: Ureteral stent placement is a key urologic procedure used to manage ureteral obstructions. It is usually performed under general anesthesia (GA) with its inherent risks. The objective was to evaluate safety, feasibility and tolerance of ureteral stent placement under local anesthesia (LA) in women. MATERIALS AND METHODS: From January 2010 to January 2013, we prospectively and consecutively reviewed all female patients who had an urgent retrograde ureteral stent placement under LA. Only primary stent placements were included in the study. Pain was assessed after surgery by Visual Analog Scale (VAS) and pain and comfort assessment during stent placement were reported. We compared outcomes and tolerance with patients under general anesthesia (GA) matched by age and operatives indications during the same period. RESULTS: We included 36 patients (18 under LA and 18 under GA) with a mean age of 59.4 +/- 22.4 years. The mean operative time was 24.4 +/- 12.9 min and 18.8 +/- 6.5 min in LA group and GA group (p = 0.110), respectively. One patient needed GA due to a poor tolerance. The mean perioperative VAS scores under LA and GA were 5.89 +/-2.95 and 2.06 +/- 2.67 (p < 0.0001), respectively. There were no intraoperative complications in either group. The procedure was painful for 16 (88.8%) patients from the LA group and 9 (50%) patients would not accept to undergo this intervention under LA again. CONCLUSION: Ureteral stent placement under LA in women can be performed safely and effectively. However, this procedure is painful and should be proposed only to selected cases