Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill

The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae

Forschungsdaten und Bibliometrie: Neue Services für die Wissenschaft

Die gezielte Unterstützung universitärer Forschung ist für Universitätsbibliotheken keine neue Herausforderung, denn die bedarfsgerechte Erwerbung und Erschließung relevanter Fachinformationen sowie die Gewährleistung des Zugangs zu den benötigten Medien sind ihre zentralen Aufgaben. Neu an dieser Herausforderung sind die schier unerschöpflichen Möglichkeiten der Informationsversorgung, die aus der digitalen Medienrevolution und der rasanten Entwicklung der Informationstechnologie erwachsen. Die Wissenschaftler/-innen erwarten einen umfassenden, schnellen, komfortablen und jederzeit störungsfreien Zugang zu den Informationsquellen. Der direkte Weg vom bibliographischen Nachweis aus Katalogen und Datenbanken zum elektronisch verfügbaren Volltext wird – mindestens bei den MINT-Fächern (Mathematik, Informatik, Naturwissenschaften, Technik) – mittlerweile als Standard angesehen. Bibliothekarische Angebote wie Schulungen zur Förderung der Informations- und Medienkompetenz, Literaturverwaltung, Publikationsserver haben das bibliothekarische Portfolio in den letzten Jahren erweitert und zählen inzwischen zum bibliothekarischen Alltagsgeschäft

Grundlinien der Wirtschaftsentwicklung 2010/2011

Das DIW Berlin rechnet für 2010 und 2011 mit einem Wirtschaftswachstum von jeweils rund zwei Prozent. Maßgebliche Triebkräfte kommen von der Binnennachfrage, die - mit Ausnahme der Unternehmensinvestitionen - in großem Umfang durch staatliche Stabilisierungsprogramme sowie durch die automatischen Stabilisatoren gestützt wird. Die wichtigste Säule bildet der private Verbrauch, der von beträchtlichen Kaufkraftzuwächsen der privaten Haushalte profitiert. Für die Exporte ist zunächst noch mit keiner kräftigen Erholung zu rechnen. Die deutschen Ausfuhren dürften aufgrund der Spezialisierung auf Investitionsgüter und des noch relativ geringen Marktanteils in den Wachstumszentren der Weltwirtschaft nur mit Verzögerung - und damit erst im nächsten Jahr - deutlicher am weltwirtschaftlichen Aufschwung teilhaben. Die Zahl der Arbeitslosen wird im kommenden Jahr zwar die Vier-Millionen-Marke übersteigen, angesichts der vorausgegangenen Produktionseinbrüche fällt der Beschäftigungsrückgang jedoch vergleichsweise schwach aus. Ermöglicht wird dies durch eine schwache Produktivitätsentwicklung und eine nur allmähliche Normalisierung der geleisteten Arbeitszeit. Gleichzeitig bleiben die Preise mit einer Inflationsrate um ein Prozent weitgehend stabil. Voraussetzung hierfür ist jedoch eine Beruhigung auf den Rohstoffmärkten, die in der Prognose unterstellt ist. Insgesamt sind die Rückschläge durch die schwere Wirtschaftskrise indes noch nicht überwunden: Erst gegen Ende 2011 dürfte die Wirtschaftskraft Deutschlands wieder an den Wert von Mitte 2008 und damit an das Niveau vor den dramatischen Produktionseinbrüchen heranreichen. Das entspricht rein rechnerisch mehr als drei Jahren mit Nullwachstum. In der Geldpolitik stellt sich die Frage nach dem richtigen Zeitpunkt für einen Ausstieg aus dem expansiven Kurs. Angesichts der noch bestehenden Unsicherheiten bezüglich der weiteren konjunkturellen Erholung und der Nachhaltigkeit der Finanzmarktstabilisierung ist eine nur allmähliche Rückführung der übermäßigen Liquiditätsversorgung empfehlenswert - zumal das Preisstabilitätsziel derzeit nicht gefährdet ist. Die Haushalts- und Finanzpolitik der Bundesregierung ist kritisch zu bewerten: Die Vorhaben der Bundesregierung - Abgabensenkung, Steuerreform, Gesundheitsreform und Einhaltung der Schuldenbremse ab 2016 - mögen für sich genommen jeweils eine gewisse Begründung haben, als Ganzes betrachtet sind diese Maßnahmen jedoch nicht gleichzeitig realisierbar. Diese Widersprüchlichkeit in der Wirtschaftspolitik kann erheblich zur Verunsicherung der privaten Haushalte und der Unternehmen beitragen. Hier wären eine stärkere Prioritätensetzung und eine klarere Gesamtkonzeption dringend geboten.Economic outlook, Business cycle forecast

Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes

Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Dynamics of nitrification in deep oligotrophic Lake Constance

(“Thaumarchaeota”) are important players in nitrification by oxidizing ammonia to nitrite, the first and rate-limiting step of nitrification. They are known to thrive best in oligotrophic environments, where they compete against their bacterial counterparts. Quantitative PCR, meta-genomics, and -transcriptomics were applied to study their abundance and activity throughout an annual cycle in the hypolimnion of deep oligotrophic Lake Constance, Germany. Moreover, nitrification rates were measured with stable isotopes and single-cell ammonia assimilation rates. In the hypo-limnion, a clonal ammonia-oxidizing archaeal population with a mean of 4.3 × 104 amoA copies ml–1 was found which reached a maximum relative abundance of 39% in summer. Phylogenetically, this population is affiliated with a new freshwater-brackish clade, distinct from related marine Nitroso-pumilus relatives. The name “Candidatus Nitrosopumilus limneticus” was proposed for this newly discovered species, which occurs in major inland water bodies around the world. Abundance and expression patterns of Ca. Nitrosopumilus limneticus were one to two orders of magnitude higher than for ammonia-oxidizing bacteria. Genes encoding the individual subunits of the ammonia mono-oxygenase were among the most highly expressed genes, supporting the involvement of the limnic Ca. Nitrosopumilus limneticus in nitrification. Correspondingly, overall nitrification rates of around 6.0 ± 0.9 nmol l–1 d–1 in the hypolimnion can be attributed mainly to this single archaeal species with cell-specific rates of 0.21 ± 0.11 fmol ammonia cell–1 d–1. Furthermore, stable isotope activity measure-ments with 15N-ammonia showed that Nitrososphaeria assimilated significantly more ammonia than other hypolimnic microorganisms. On average, 12% of the total assimilated ammonia by the microbial community in the hypolimnion is taken up by Ca. Nitrosopumilus limneticus. Each year 1.76 × 109 g NH4+ is oxidized by ammonia oxidizers in the hypolimnion of Lake Constance, which corresponds to 11% of N-biomass produced by phytoplankton every year. Autotrophic Nitrososphaeria use hydrogen carbonate for their carbon demand. Based on transcription levels of their carbon fixation genes, Nitrososphaeria are in the same range as nitrite oxidizers, cyanobacteria and an alphaproteobacterial RubisCO cluster in the hypolimnion. The all-encompassing dominant autotroph in the hypolimnion based on transcription levels, was related to a cryptophyte, which is hypothesized to be a symbiont of a ciliate species. Accordingly, Ca. Nitrosopumilus limneticus has less of an impact on the carbon cycle than the nitrogen cycle. In conclusion, this study showed that Ca. Nitrosopumilus limneticus is nearly the sole ammonia oxidizer in oligotrophic Lake Constance, strongly contributing to the removal of ammonia in lake water, and in turn, accomplish an essential ecosystem service for safe drinking water supply.publishe

Temperature and oxygen measurements in Lake Constance, Germany

This dataset is part of a study investigating the freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. It includes monthly measurements of temperature and oxygen in the whole water column (0-132 m) in Lake Constance (Germany) from November 2017 to November 2019. The probes, which were used, derived from Sea & Sun Technology GmbH, Trappenkamp, Germany or bbe Moldaenke GmbH or RBR Ltd.; Ottawa, Canada

Chlorophyll a concentrations in Lake Constance, Germany

This dataset is part of a study investigating the freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. It includes biweekly-monthly measurements of chlorophyll a concentrations in the upper water column (0-60 m) in Lake Constance (Germany) from November 2017 to November 2019. Water was taken with a Niskin bottle and filtered on board directly using Glasfiber filters

Ammonium and nitrate concentrations in Lake Constance, Germany

This dataset is part of a study investigating the freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. It includes monthly measurements of nitrate and ammonia concentrations in the whole water column (1-135 m) in Lake Constance (Germany) from November 2017 to November 2019. Water was taken with a Niskin bottle and pre-filtered on board directly through 0.2µm. The indicated time represents the sampling time

Archaeal nitrification in Lake Constance, Germany

The aim of this work was to study freshwater Nitrososphaeria and their impact on the nitrogen cycling in lakes. We followed their absolute abundance in oligotrophic Lake Constance (Germany) with quantitative polymerase chain reaction (qPCR) over a time frame of two consecutive years from November 2017 until November 2019. During this time we took water samples monthly (2017/2018) or as required (2019) at a depth of 85 m. We combined this data with measurements of nitrate and ammonia concentrations in the whole water column. In addition, we performed stable isotope experiments with addition of 15N-ammonium in 2019 to analyze nitrification rate in the hypolimnion of Lake Constance. The bundled publication also includes measurements of chlorophyll a concentrations in the upper water column and measurements of temperature and oxygen in the whole water column