Microbiological communities of North Atlantic, 3rd Dimension of the Logatchev-Hydrothermalfield - Cruise No. MSM03 of Research Vessel Maria S. Merian

Fahrtabschnitt MSM 03/1: Der nördliche Atlantik weist drei Eigenschaften auf, die ihn zu einem der interessantesten Meeresgebiete machen. Zum einen beginnt hier das Absinken von kalten und dichten Wassermassen nördlich von Grönland und Island und bildet dadurch einen wichtigen Faktor der globalen ozeanischen Wasserzirkulation, dem globalen Strömungsgürtel. Zum anderen transportiert die Verlängerung des Golf Stromes, die Nordatlantische Drift, warmes Oberflächenwasser bis nach Spitzbergen und beeinflußt so entscheidend das Klima in Europa. Schließlich fließen kalte Oberflächenwässer an der Küste Grönlands entlang südwärts und transportieren nährstoffreiches Wasser in den Süden. Während der letzten 15 Jahre ist mit Hilfe von kultivierungsunabhängigen Methoden die mikrobiellen Gemeinschaften in verschiedenen marinen Systemen sehr intensiv erforscht worden. Viele unbekannte und nicht kultivierte Organismen wie der weit verbreitete SAR11 Cluster wurden entdeckt und quantitativ verfolgt. Kürzlich wurden Genomanalysen ganzer mikrobieller Gemeinschaften initiiert (Metagenomics). Jedoch bleibt solche Forschung oft auf küstennahe Standorte beschränkt. Nur wenige Studien beschrieben bisher die mikrobielle Diversität, Struktur und Funktion im offenen Ozean und über ganze Meeresbecken hinweg. Das sogenannte AMT (Atlantic Meridional Transect) Programm ist eines dieser Studien, welche es sich zur Aufgabe gemacht hat, den gesamten Atlantischen Ozean von den britischen Inseln (50°N) bis zu den Falkland Inseln (50°S) zu untersuchen. Zweimal im Jahr werden in einem interdisziplinären Ansatz der Einfluß der biotischen (Phytoplankton, Zooplankton, Mikrobiologie) und abiotischen Faktoren (physikalischen und chemischen Parameter) auf die gesamte mikrobielle Gemeinschaft untersucht. Erste Ergebnisse dieser Studien bestätigten zum Beispiel die Einnischung von verschiedenen Ökotypen des wichtigen Primärproduzenten Prochlorococcus in distinkte Wasserkörper (Tiefe, Breitengrad) entlang des Atlantischen Ozeans. Eine erste Studie zur Erforschung des Picoplanktons nördlich des 50° Breitengrades stellte das PRIME Programm dar. Neuere Untersuchungen in dem Gebiet richteten sich auf die Bakterioplankton-Gemeinschaft von Tiefenwässern unterhalb von 1000 m. Für die Oberflächengewässer dieser Region jedoch fehlt eine genauere Untersuchung der Diversität, Struktur und Funktion der mikrobiellen Gemeinschaft mit modernen molekularbiologischen Methoden. Fahrtabschnitt MSM 03/2: Das Ziel der Forschungsfahrt ist die detaillierte Untersuchung des flachen Untergrundes im Logatchev Hydrothermalfeldam Mittelatlantischen Rücken (MAR) bei 15°N mit bis zu 15 m tiefen Bohrungen. Die Fahrt findet im Rahmen des DFG-SPP 1144 statt und komplettiert die bisher gewonnenen Oberflächenproben sowie die im Rahmen des ODP-Leg 209 gewonnenen Tiefen-proben. Das in 3000m Wassertiefe liegende und an Mantelgesteine gebundene Logatchev Hydrothermalfeld ist durch intensive Anreicherung an Kupfer, Gold, Kobalt und anderen Wertelementen am Meersboden und vermutlich auch im flachen Untergrund gekennzeichnet. Gleichzeitig sind die hydrothermalen Fluide an bestimmten Gasen wie CH4 und H2 sehr stark angereichert, was intensive Auswirkungen auf die an das Hydrothermalsystem gekoppelten Mikroorganismen hat. Die Mikroben sitzen auf den Oberflächen der Untergrundgesteine und Mineralpräzipitate im Bereich der hydrothermalen Austrittsstellen, wobei letztere spezifische ökologische Nischen bilden. Neben der Untersuchung der Tiefenzonierungen der Mineralisationen und Alterationen sowie deren Altersstellungen, ist die vermutete direkte Interaktion zwischen den Mikroorganismen (subsurface biosphere) und den hydrothermalen Mineralbildungen ein weiterer wichtiger wissenschaftlicher Aspekt. Auf der MSM03/2-Reise wird erstmals das ferngesteuerte Bohrgerät Rockdrill2 des British Geological Survey eingesetzt. Neben deutschen Wissenschaftlern der Fachrichtungen Lagerstättenkunde, Petrologie, Geochemie und Mikrobiologie werden britische Techniker und Ingenieure sowie Wissenschaftler aus Russland und China an der Fahrt teilnehmen.Leg MSM 03/1 The North Atlantic Ocean has three features which makes it one of the most interesting parts of the world’s oceans. First, the extensive downwelling of cold and dense water masses north of Greenland and Iceland mark an important point in the global ocean water circulation, known as the “global conveyer belt”. Second, the extension of the Gulf Stream, the North Atlantic drift, is transporting warm surface water masses to high latitudes up to Spitzbergen thereby significantly influencing the climate of Europe. Third, cold surface water masses flow southwards along the coast of Greenland transporting nutrient rich waters to the south. The components of the microbial community inhabiting different marine systems have been intensively investigated by cultivation independent methods over the past 15 years. Many unknown and yet-uncultured organisms like the ubiquous SAR11 cluster have been detected and quantitatively monitored. Recently genomic analysis of whole microbial communities (=metagenomics) have been initiated. However such research is often restricted to few sites or limited to near-shore sites. Only few open ocean and basin – scale studies of the microbial community diversity, structure and function have been conducted so far. One of these studies is the British Atlantic Meridional Transect (AMT) program, which monitors the entire Atlantic Ocean from the app. 50°S (Falkland Islands) to app. 50°N (United Kingdom) twice a year. By an integrated approach of many disciplines including physical and chemical oceanography, microbiology, phytoplankton and zooplankton research the variability of microorganisms and the biotic and abiotic factors are studied. First results confirmed, for example, the nichepartitioning of different ecotypes of the imprimary producer Prochlorococcus in distinct water layers (depth, latitude) across the Atlantic Ocean. A first study of the picoplankton community north of 50°N of the Atlantic Ocean was done in 1996 during the PRIME cruise. Recent studies in the same area have focused on the bacterioplankton community of deep water masses below 1000 m water depths. An in-depth analysis of the diversity, structure and function of the microbial community in the photic layer down to genus and group level wit modern molecular tools was not yet conducted for this area. Leg MSM 03/2 The main objective of this cruise is the investigation of the shallow subsurface in the Logatchev hydrothermal field on the Mid Atlantic Ridge at 15°N by drilling up to 15 m deep cores. The cruise will take place within the DFG-SPP 1144 and will complete the surface sampling realized so far as well as deep sampling carried out by ODP Leg 209. The ultramafic-hosted Logatchev hydrothermal field situated in 3000m water depth is characterized by large enrichments of Cu, Au, Co, and other valuable elements at the seafloor and supposedly in the shallow subsurface. Hydrothermal fluids are largely enriched in certain gases like CH4 and H2 which is clearly linked to the microbiology associated with this hydrothermal system. The surfaces of rocks and minerals in the subsurface of the hydrothermal vent systems represent specific ecological niches for microorganisms which will be found associated to these interfaces. Apart from the investigation of the depth zonations of the mineralization and alteration as well as their age relationships is the establishmentof the variability of the subsurface biosphere and their supposed direct influence on the formation and transformation of hydrothermal mineral precipitations another major scientific aspect of the project. As drilling device the newly built, remotely operated Rockdrill2 of the British Geological Survey in Edinburgh (UK) will be used. Scientists from Germany representing the fields of economic geology, petrology, geochemistry and microbiology, technicians and engineers from UK as well as scientists from Russia and China will take part in the cruise

A pipeline for targeted metagenomics of environmental bacteria.

BackgroundMetagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses.MethodsCells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity.ResultsPure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade.ConclusionsWith the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades. Video abstract

A Chlorophyll-Derived Phylloxanthobilin Is a Potent Antioxidant That Modulates Immunometabolism in Human PBMC

Phyllobilins are natural products derived from the degradation of chlorophyll, which proceeds via a common and strictly controlled pathway in higher plants. The resulting tetrapyrrolic catabolites-the phyllobilins-are ubiquitous in nature;despite their high abundance, there is still a lack of knowledge about their physiological properties. Phyllobilins are part of human nutrition and were shown to be potent antioxidants accounting with interesting physiological properties. Three different naturally occurring types of phyllobilins-a phylloleucobilin, a dioxobilin-type phylloleucobilin and a phylloxanthobilin (PxB)-were compared regarding potential antioxidative properties in a cell-free and in a cell-based antioxidant activity test system, demonstrating the strongest effect for the PxB. Moreover, the PxB was investigated for its capacity to interfere with immunoregulatory metabolic pathways of tryptophan breakdown in human blood peripheral mononuclear cells. A dose-dependent inhibition of tryptophan catabolism to kynurenine was observed, suggesting a suppressive effect on pathways of cellular immune activation. Although the exact mechanisms of immunomodulatory effects are yet unknown, these prominent bioactivities point towards health-relevant effects, which warrant further mechanistic investigations and the assessment of the in vivo extrapolatability of results. Thus, phyllobilins are a still surprisingly unexplored family of natural products that merit further investigation

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs

“Pomacytosis” — Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae

The smallest algae, less than 3 μm in diameter, are the most abundant eukaryotes of the World Ocean. Their feeding on planktonic bacteria of similar size is globally important but physically enigmatic. Tiny algal cells, tightly packed with the voluminous chloroplasts, nucleus, and mitochondriaon, appear to have insufficient organelle-free space for prey internalization. Here, we present the first direct observations of how the 1.3- μm algae, which are only 1.6 times bigger in diameter than their prey, hold individual Prochlorococcus cells in their open hemispheric cytostomes. We explain this semi-extracellular phagocytosis by the cell size limitation of the predatory alga, identified as the Braarudosphaera haptophyte with a nitrogen (N2)–-fixing endosymbiont. Because the observed semi-extracellular phagocytosis differs from all other types of protistan phagocytosis, we propose to name it “pomacytosis” (from the Greek πώμα for “plug”)

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea

The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations

In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls

Net growth of microbial populations, i.e., changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate the cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8 d-1 and Aurantivirga of up to 1.9 d-1 differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9 d-1, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5 d-1) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within one day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls

Evidence for a Two-stage Melting Transition of the Vortex Matter in Bi2Sr2Ca1Cu2O8+d Single Crystals obtained by Muon Spin Rotation

From muon spin rotation measurements on under- to overdoped Bi-2212 crystals we obtain evidence for a two-stage transition of the vortex matter as a function of temperature. The first transition is well known and related to the irreversibility line (IL). The second one is located below the IL and has not been previously observed. It occurs for all three sets of crystals and is unrelated to the vortex mobility. Our data are consistent with a two-stage melting scenario where the intra-planar melting of the vortex lattice and the inter-planar decoupling of the vortex lines occur independently.Comment: 9 pages and 3 figure

Особенности формирования структуры ЗТВ и зон оплавления покрытия на основе стали 10Р6М5 электронным лучом в вакууме

Особенности формирования структуры в зоне оплавления и зоне термического влияния композиционного покрытия на основе стали 10Р6М5 в ходе вакуумного импульсного электронного воздействияEigenschaften der Strukturbildung in der Schmelzzone und die Warmeeinflu?zone, auf der Grundlage der Warme einflus sverbundbeschichtung 10Р6M5 Stahl wahrend der Vakuumbelichtungsgepulster Elektronenstrah

Scientific Opportunities with an X-ray Free-Electron Laser Oscillator

An X-ray free-electron laser oscillator (XFELO) is a new type of hard X-ray source that would produce fully coherent pulses with meV bandwidth and stable intensity. The XFELO complements existing sources based on self-amplified spontaneous emission (SASE) from high-gain X-ray free-electron lasers (XFEL) that produce ultra-short pulses with broad-band chaotic spectra. This report is based on discussions of scientific opportunities enabled by an XFELO during a workshop held at SLAC on June 29 - July 1, 2016Comment: 21 pages, 12 figure