Cruise Report RV Poseidon Cruise No. P 475 [POS475]

Dates of the cruise: from 27. 9. to 12. 10. 2014. - Purpose of the cruise: Investigation of transport, deposition and exchange of matter at the sediment-water boundary in German waters (Project SECOS). Reconstruction of Holocene history of the western Baltic Sea (Gdansk-Basin and Bornholm Basin). Acoustic mapping of the sea floor at selected areas in German waters. Documentation and sampling of “stone reef habitats” by research scuba divers (German waters only)

Endolithic Algae Affect Modern Coral Carbonate Morphology and Chemistry

While burial diagenetic processes of tropical corals are well investigated, current knowledge about factors initiating early diagenesis remains fragmentary. In the present study, we focus on recent Porites microatolls, growing in the intertidal zone. This growth form represents a model organism for elevated sea surface temperatures (SSTs) and provides important but rare archives for changes close to the seawater/atmosphere interface with exceptional precision on sea level reconstruction. As other coral growth forms, microatolls are prone to the colonization by endolithic green algae. In this case, the algae can facilitate earliest diagenetic alteration of the coral skeleton. Algae metabolic activity not only results in secondary coral porosity due to boring activities, but may also initiate reprecipitation of secondary aragonite within coral pore space, a process not exclusively restricted to microatoll settings. In the samples of this initial study, we quantified a mass transfer from primary to secondary aragonite of around 4% within endolithic green algae bands. Using δ 18 O, δ 13 C, Sr/Ca, U/Ca, Mg/Ca, and Li/Mg systematics suggests that the secondary aragonite precipitation followed abiotic precipitation principles. According to their individual distribution coefficients, the different isotope and element ratios showed variable sensitivity to the presence of secondary aragonite in bulk samples, with implications for microatoll-based SST reconstructions. The secondary precipitates formed on an organic template, presumably originating from endolithic green algae activity. Based on laboratory experiments with the green algae Ostreobium quekettii, we propose a conceptual model that secondary aragonite formation is potentially accelerated by an active intracellular calcium transport through the algal thallus from the location of dissolution into coral pore spaces. The combined high-resolution imaging and geochemical approach applied in this study shows that endolithic algae can possibly act as a main driver for earliest diagenesis of coral aragonite starting already during a coral’s life span

Effect of large magnetotactic bacteria with polyphosphate inclusions on the phosphate profile of the suboxic zone in the Black Sea

The Black Sea is the world’s largest anoxic basin and a model system for studying processes across redox gradients. In between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10–40 m, where neither oxygen nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak, as they contain 26–34% phosphorus compared to only 1–5% in metal-rich particles. Furthermore, we found increased gene expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.We are grateful for the competent technical assistance of Ronny Baaske, Christian Burmeister, Christin Laudan and Christian Meeske. We are greatly indebted to Cindy Lee and Bo Barker Jørgensen for providing extremely helpful comments on an earlier version of the manuscript. Horst D. Schulz and René Friedland are acknowledged for stimulating discussions on the modeling approach. We thank the captain and the crew of the R/V “Maria S. Merian” for the excellent support on board and the DFG (MSM33) and BMBF (01DK12043) for financing the cruise. The particle analysis was funded by the BMBF (03F0663A). S.B. was funded by a BONUS BLUEPRINT project (03F0679A awarded to KJ; http://blueprint- project.org), supported by BONUS (Art 185), funded jointly by the EU and the German Federal Ministry of Education and Research (BMBF). T. S. was funded by the German research foundation (DFG) (awarded to K.J., JU 367/16-1). Metagenome sequencing was done at the Swedish National Genomics Infrastructure (NGI) at SciLifeLab (Sweden).We are grateful for the competent technical assistance of Ronny Baaske, Christian Burmeister, Christin Laudan and Christian Meeske. We are greatly indebted to Cindy Lee and Bo Barker Jørgensen for providing extremely helpful comments on an earlier version of the manuscript. Horst D. Schulz and René Friedland are acknowledged for stimulating discussions on the modeling approach. We thank the captain and the crew of the R/V “Maria S. Merian” for the excellent support on board and the DFG (MSM33) and BMBF (01DK12043) for financing the cruise. The particle analysis was funded by the BMBF (03F0663A). S.B. was funded by a BONUS BLUEPRINT project (03F0679A awarded to KJ; http://blueprint- project.org), supported by BONUS (Art 185), funded jointly by the EU and the German Federal Ministry of Education and Research (BMBF). T. S. was funded by the German research foundation (DFG) (awarded to K.J., JU 367/16-1). Metagenome sequencing was done at the Swedish National Genomics Infrastructure (NGI) at SciLifeLab (Sweden)

Incorporation of minor and trace elements into cultured brachiopods : implications for proxy application with new insights from a biomineralisation model

his project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 643084 (BASE-LiNE Earth), and was also supported by the collaborative research initiative CHARON (DFG Research Group 1644 – Phase II) funded by the German Research Foundation.Brachiopods present a key fossil group for Phanerozoic palaeo-environmental and palaeo-oceanographical reconstructions, owing to their good preservation and abundance in the geological record. Yet to date, hardly any geochemical proxies have been calibrated in cultured brachiopods and only little is known on the mechanisms that control the incorporation of various key elements into brachiopod calcite. To evaluate the feasibility and robustness of multiple Element/Ca ratios as proxies in brachiopods, specifically Li/Ca, B/Ca, Na/Ca, Mg/Ca, Sr/Ca, Ba/Ca, as well as Li/Mg, we cultured Magellania venosa, Terebratella dorsata and Pajaudina atlantica under controlled experimental settings over a period of more than two years with closely monitored ambient conditions, carbonate system parameters and elemental composition of the culture medium. The experimental setup comprised of two control aquariums (pH0 = 8.0 and 8.15, T = 10 °C) and treatments where pCO2−pH (pH1 = 7.6 and pH2 = 7.35), temperature (T = 16 °C) and chemical composition of the culture medium were manipulated. Our results indicate that the incorporation of Li and Mg is strongly influenced by temperature, growth effects as well as carbonate chemistry, complicating the use of Li/Ca, Mg/Ca and Li/Mg ratios as straightforward reliable proxies. Boron partitioning varied greatly between the treatments, however without a clear link to carbonate system parameters or other environmental factors. The partitioning of both Ba and Na varied between individuals, but was not systematically affected by changes in the ambient conditions. We highlight Sr as a potential proxy for DIC, based on a positive trend between Sr partitioning and carbonate chemistry in the culture medium. To explain the observed dependency and provide a quantitative framework for exploring elemental variations, we devise the first biomineralisation model for brachiopods, which results in a close agreement between modelled and measured Sr distribution coefficients. We propose that in order to sustain shell growth under increased DIC, a decreased influx of Ca2+ to the calcifying fluid is necessary, driving the preferential substitution of Sr2+ for Ca2+ in the crystal lattice. Finally, we conducted micro-computed tomography analyses of the shells grown in the different experimental treatments. We present pore space – punctae – content quantification that indicates that shells built under increased environmental stress, and in particular elevated temperature, contain relatively more pore space than calcite, suggesting this parameter as a potential novel proxy for physiological stress and even environmental conditions.Publisher PDFPeer reviewe

The crystal structure of the Thermus aquaticus DnaB helicase monomer

The ring-shaped hexameric DnaB helicase unwinds duplex DNA at the replication fork of eubacteria. We have solved the crystal structure of the full-length Thermus aquaticus DnaB monomer, or possibly dimer, at 2.9 Å resolution. DnaB is a highly flexible two domain protein. The C-terminal domain exhibits a RecA-like core fold and contains all the conserved sequence motifs that are characteristic of the DnaB helicase family. The N-terminal domain contains an additional helical hairpin that makes it larger than previously appreciated. Several DnaB mutations that modulate its interaction with primase are found in this hairpin. The similarity in the fold of the DnaB N-terminal domain with that of the C-terminal helicase-binding domain (HBD) of the DnaG primase also includes this hairpin. Comparison of hexameric homology models of DnaB with the structure of the papillomavirus E1 helicase suggests the two helicases may function through different mechanisms despite their sharing a common ancestor

Family Size and Turnover Rates among Several Classes of Small Non–Protein-Coding RNA Genes in Caenorhabditis Nematodes

It is important to understand the forces that shape the size and evolutionary histories of gene families. Here, we investigated the evolution of non–protein-coding RNA genes in the genomes of Caenorhabditis nematodes. We specifically focused on nested arrangements, that is, cases in which an RNA gene is entirely contained in an intron of another gene. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. Two distinct patterns are evident in the data. Genes encoding small nuclear RNAs (snRNAs) and transfer RNAs form large families, which have persisted since before the common ancestor of Metazoa. Yet, individual genes die relatively rapidly, with few orthologs having survived since the divergence of Caenorhabditis elegans and Caenorhabditis briggsae. In contrast, genes encoding small nucleolar RNAs (snoRNAs) are either single-copy or form small families. Individual snoRNAs turn over at a relatively slow rate—most C. elegans genes have clearly identifiable orthologs in C. briggsae. We also found that in Drosophila, genes from larger snRNA families die at a faster rate than their counterparts from single-gene families. These results suggest that a relationship between family size and the rate of gene turnover may be a general feature of genome evolution