A database of marine phytoplankton abundance, biomass and species composition in Australian waters

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

International audienceDes connaissances approfondies sur la variation spatiale et temporelle de la diversité et de la fonction microbiennes sont nécessaires pour une meilleure compréhension des réponses écologiques et évolutives au changement global. En particulier, l'étude de l'ancien ADN microbien conservé dans les archives sédimentaires des lacs et des océans peut nous aider à évaluer les réponses des microbes aquatiques dans le passé et à faire des prédictions sur les changements futurs de la biodiversité dans ces écosystèmes. Les progrès récents des méthodes de génétique moléculaire appliquées à l'analyse de l'ADN historiquement déposé dans les sédiments ont non seulement permis l'identification taxonomique des communautés microbiennes aquatiques passées, mais également permis de retracer leur évolution et leur adaptation aux perturbations épisodiques et aux changements environnementaux progressifs. Néanmoins, certains défis demeurent pour que les scientifiques tirent pleinement parti du domaine en développement rapide de la paléogénétique, notamment la capacité limitée à détecter des taxons rares et à reconstruire des génomes complets pour des études évolutives. Ici, nous fournissons un bref examen de certaines des avancées récentes dans le domaine de la paléomicrobiologie environnementale et discutons des défis restants liés à l'application de méthodes de génétique moléculaire pour étudier la diversité microbienne, l'écologie et l'évolution dans les archives de sédiments. Nous prévoyons que, dans un avenir proche, la paléomicrobiologie environnementale apportera un nouvel éclairage sur les processus d'évolution du génome microbien et les réponses de l'écosystème microbien aux changements environnementaux du Quaternaire à un niveau de détail sans précédent. Ces informations peuvent, par exemple, contribuer aux reconstructions géologiques des cycles biogéochimiques et prédire les réponses des écosystèmes aux perturbations environnementales, y compris dans le contexte des changements globaux induits par l'homme

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes

The effect of red blood cell transfusion on tissue oxygenation and microcirculation in severe septic patients

BACKGROUND: Microcirculation plays a vital role in the development of multiple organ failure in severe sepsis. The effects of red blood cell (RBC) transfusions on these tissue oxygenation and microcirculation variables in early severe sepsis are not well defined. METHODS: This is a prospective, observational study of patients with severe sepsis requiring RBC transfusions of one to two units of non-leukoreduced RBCs for a hemoglobin < 7.0, or for a hemoglobin between 7.0 and 9.0 with lactic acidosis or central venous oxygen saturation < 70%. This study took place in a 54-bed, medical-surgical intensive care unit of a university-affiliated hospital. Thenar tissue oxygen saturation was measured by using a tissue spectrometer on 21 patients, and a vaso-occlusive test was performed before and 1 hour after transfusion. The sublingual microcirculation was assessed with a Sidestream Dark Field device concomitantly on 11 of them. RESULTS: RBC transfusion resulted in increase in hemoglobin (7.23 (± 0.87) to 8.75 (± 1.06) g/dl; p < 0.001). RBC transfusion did not globally affect near-infrared spectrometry (NIRS)-derived variables. However, percent change in muscle oxygen consumption was negatively correlated with baseline (r = - 0.679, p = 0.001). There was no statistically significant correlation between percent change in vascular reactivity and baseline (p = 0.275). There was a positive correlation between percent change in oxygen consumption and percent change in vascular reactivity (r = 0.442, p = 0.045). In the 11 patients, RBC transfusion did not globally affect NIRS-derived variables or SDF-derived variables. There was no statistically significant correlation between percent change in small vessel perfusion and baseline perfusion (r = -0.474, p = 0.141), between percent change in small vessel flow and baseline flow (r = -0.418, p = 0.201), or between percent change in small vessel perfusion and percent change in small vessel flow (r = 0.435, p = 0.182). CONCLUSIONS: In a small sample population, muscle tissue oxygen consumption, microvascular reactivity and sublingual microcirculation were globally unaltered by RBC transfusion in severe septic patients. However, muscle oxygen consumption improved in patients with low baseline and deteriorated in patients with preserved baseline. Future research with larger samples is needed to further examine the association between RBC transfusion and outcomes of patients resuscitated early in severe sepsis, with an emphasis on elucidating the potential contribution of microvascular factors