Molecular fingerprinting and amplicon sequencing of the bacterial biofilm on settlement tiles deployed along natural pH gradients in Papua New Guinea

Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps, and upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis were used to characterize more than 200 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga, whereas putative settlement-inducing taxa only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous with approximately 25% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a weak effect on community composition (R² ~ 1%) and did not affect community richness and evenness. In contrast, there were strong differences between upper and lower surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms than changes in seawater pH.

(Table 2) Trace element composition of seleceted clast and matrix materials from ODP Site 125-786

Shipboard examination of volcanic and sedimentary strata at Site 786 suggested that at least four types of breccias are present: flow-top breccias, associated with cooling and breakup on the upper surface of lava flows; autobreccias, formed by in-situ alteration at the base of flows; fault-gouge breccias; and true sedimentary breccias derived from weathering and erosion of underlying flows. It is virtually impossible to assess the origin of breccia matrix by textural and mineralogical analyses alone. However, it is fundamental for our understanding of breccia provenance to determine the source component of the matrix material. Whether the matrix is uniquely clastderived can be determined by geochemical fingerprinting. Trace elements that are immobile during weathering and alteration do not change their relative abundances. A contribution to the matrix from any source with an immobile trace element signature different from that of the clasts would appear as a perturbation of the trace element signature of the matrix. Trace element analysis of bulk samples from clasts and matrix material in individual breccia units was undertaken in a fashion similar to that used by Brimhall and Dietrich (1987, doi:10.1016/0016-7037(87)90070-6) in analyzing soil provenance: (1) to help distinguish between sedimentary and volcanic breccias, (2) to determine the degree of mixing and depth of erosion in sedimentary breccias, and (3) to analyze the local provenance of the individual breccia components (matrix and clasts). The following elements were analyzed by X-ray fluorescence (XRF): Rb, Sr, Ba, U, Zr, Cu, Zn, Ti, Cr, and V. Of these elements, Zr and Ti probably exhibit truly immobile behavior (Humphris and Thompson, 1978, doi:10.1016/0016-7037(78)90222-3 ). The remaining elements are useful as a reference for the extent of compositional change during the formation of matrix material (Brimhall and Dietrich, 1987, doi:10.1016/0016-7037(87)90070-6).

Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

(Appendix A) Geochemical composition of snow and eolian mineral dust from Berkner Island ice sheet, Antarctica

The Sr and Nd isotopic composition of dust extracted from recent snow layers at the top of Berkner Island ice sheet (located within the Filchner-Ronne Ice Shelf at the southern end of the Weddell Sea) enables us, for the first time, to document dust provenance in Antarctica outside the East Antarctic Plateau (EAP) where all previous studies based on isotopic fingerprinting were carried out. Berkner dust displays an overall crust-like isotopic signature, characterized by more radiogenic 87Sr/86Sr and much less radiogenic 143Nd/144Nd compared to dust deposited on the EAP during glacial periods. Differences with EAP interglacial dust are not as marked but still significant, indicating that present-day Berkner dust provenance is distinct, at least to some extent, from that of the dust reaching the EAP. The fourteen snow-pit sub-seasonal samples that were obtained span a two-year period (2002-2003) and their dust Sr and Nd isotopic composition reveals that multiple sources are at play over a yearly time period. Southern South America, Patagonia in particular, likely accounts for part of the observed spring/summer dust deposition maxima, when isotopic composition is shifted towards 'younger' isotopic signatures. In the spring, possible additional inputs from Australian sources would also be supported by the data. Most of the year, however, the measured isotopic signatures would be best explained by a sustained background supply from putative local sources in East Antarctica, which carry old-crust-like isotopic fingerprints. Whether the restricted East Antarctic ice-free areas produce sufficient eolian material has yet to be substantiated however. The fact that large (> 5 µm) particles represent a significant fraction of the samples throughout the entire time-series supports scenarios that involve contributions from proximal sources, either in Patagonia and/or Antarctica (possibly including snow-free areas in the Antarctic Peninsula and other areas as well). This also indicates that additional dust transport, which does not reach the EAP, must occur at low-tropospheric levels to this coastal sector of Antarctica.

Electromagnetic, rock magnetic, and geochemical properties of surficial sediments in Eckernförde Bay

Submarine groundwater discharge in coastal settings can massively modify the hydraulic and geochemical conditions of the seafloor. Resulting local anomalies in the morphology and physical properties of surface sediments are usually explored with seismo-acoustic imaging techniques. Controlled source electromagnetic imaging offers an innovative dual approach to seep characterization by its ability to detect pore-water electrical conductivity, hence salinity, as well as sediment magnetic susceptibility, hence preservation or diagenetic alteration of iron oxides. The newly developed electromagnetic (EM) profiler Neridis II successfully realized this concept for a first time with a high-resolution survey of freshwater seeps in Eckernförde Bay (SW Baltic Sea). We demonstrate that EM profiling, complemented and validated by acoustic as well as sample-based rock magnetic and geochemical methods, can create a crisp and revealing fingerprint image of freshwater seepage and related reductive alteration of near-surface sediments. Our findings imply that (1) freshwater penetrates the pore space of Holocene mud sediments by both diffuse and focused advection, (2) pockmarks are marked by focused freshwater seepage, underlying sand highs, reduced mud thickness, higher porosity, fining of grain size, and anoxic conditions, (3) depletion of Fe oxides, especially magnetite, is more pervasive within pockmarks due to higher concentrations of organic and sulfidic reaction partners, and (4) freshwater advection reduces sediment magnetic susceptibility by a combination of pore-water injection (dilution) and magnetite reduction (depletion). The conductivity vs. susceptibility biplot resolves subtle lateral litho- and hydrofacies variations.

Table 1 Microorganisms, identified with DOGE analysis. 16S rDNA sequences, obtained from sequencing of DOGE bands, were assigned to the corresponding microorganisms

Microorganisms play an important role in the transformation of material within the earth's crust. The storage of CO2 could affect the composition of inorganic and organic components in the reservoir, consequently influencing microbial activities. To study the microbial induced processes together with geochemical, petrophysical and mineralogical changes, occurring during CO2 storage, long-term laboratory experiments under simulated reservoir P-T conditions were carried out. Clean inner core sections, obtained from the reservoir region at the CO2 storage site in Ketzin (Germany) from a depth of about 650 m, were incubated in high pressure vessels together with sterile synthetic formation brine under in situ P-T conditions of 5.5 MPa and 40°C. A 16S rDNA based fingerprinting method was used to identify the dominant species in DNA extracts of pristine sandstone samples. Members of the alpha- and beta-subdivisions of Proteobacteria and the Actinobacteria were identified. So far sequences belonging to facultative anaerobic, chemoheterotrophic bacteria (Burkholderia fungorum, Agrobacterium tumefaciens) gaining their energy from the oxidation of organic molecules and a genus also capable of chemolithoautotrophic growth (Hydrogenophaga) was identified. During CO2 incubation minor changes in the microbial community composition were observed. The majority of microbes were able to adapt to the changed conditions. During CO2 exposure increased concentrations of Ca**2+, K**+, Mg**2+ and SO4**2- were observed. Partially, concentration rises are (i) due to equilibration between rock pore water and synthetic brine, and (ii) between rock and brine, and are thus independent on CO2 exposure. However, observed concentrations of Ca**2+, K**+, Mg**2+ are even higher than in the original reservoir fluid and therefore indicate mineral dissolution due to CO2 exposure.

Magnetic measurements performed on sediments from the Bay of Seine seafloor (France) from 2011 to 2013

Impact and monitoring of dredge spoils are an important environmental issue. This investigation aims to map two dredge-spoil dispersals in the Bay of Seine by using an innovative application of well-established environmental magnetic proxies. Low-field magnetic susceptibility measurements were performed on discrete samples from dredge sediments and from the Bay of Seine seafloor before & after dumping. The fingerprinting of the dispersion of dredge-dumped sediments is efficient due to the higher susceptibility of the dredge sediments with respect to the background. Besides, terrestrial input is also monitored in our susceptibility maps. Dilution of the susceptibility signal allows an estimation of the resilience of the sedimentary environment on a six-month survey. This susceptibility signal is controlled by the ferromagnetic fraction of the sediment. A constant magnetic mineralogy carried by magnetite is observed in the study area, thus a qualitative parameter for magnetic grain size was selected that shows an in-progress resilience pattern over the survey.

Seagrass biofilm communities at a naturally CO2-rich vent at Papua New Guinea

Seagrass meadows are a crucial component of tropical marine reef ecosystems. The seagrass plants are colonized by a multitude of epiphytic organisms that contribute to determining the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared to the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased abundance of bacterial types associated with coral diseases at the CO2-impacted site (Fusobacteria, Thalassomonas) whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios.

Strontium isotope ratios of plant and soil samples from France

The dataset consists of 87Sr/86Sr isotope ratios of plant samples and soil leachates covering the major geologic regions of France. In addition to the isotope data it provides the spatial context for each sample, including background geology, field observations and soil descriptions. The dataset can be used to create Sr isoscapes for France, which can be applied in a wide range of fields including archaeology, ecology, soil, food, and forensic sciences.

Porewater concentrations, pH, single cell number, anaerobic oxidation of methane (AOM) rate, sulfate reduction (SR) rate of samples during METEOR cruise M76/3b at the REGAB cold seep site from the West African margin in 2008

The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining porewater geochemistry, in situ quantification of fluxes and consumption of methane, as well bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

(Table A1) Isotopic ratios of Sr, Nd, and Pb for sediments in ODP Leg 138 sites

The provenance of eolian dust supplied to deep-sea sediments has the potential to offer insights into changes in past atmospheric circulation. Specifically, measuring temporal changes in dust provenance can shed light on changes in the mean position of the Intertropical Convergence Zone (ITCZ), a region acting as a barrier separating wind-blown material derived from northern versus southern hemisphere sources. Here we have analyzed Nd, Sr, and Pb isotope ratios in the operationally-defined detrital component extracted from deep-sea sediments in the eastern equatorial Pacific (EEP) along a meridional transect at 110°W from 3°S to 7°N (ODP Leg 138, sites 848-853). Sr isotope results show that barite Sr has a significant influence on 87Sr/86Sr isotope ratios of samples in the upwelling zone of the EEP. However, sites located >3° or more away from the equator (sites 852 and 853) are believed to not be affected by barite Sr and provide useful detrital Sr signals. 208Pb/206Pb and 207Pb/206Pb ratios in all cores fall into the Pb-isotope space of five potential dust sources (Asia, North and Central/South America, Sahara, and Australia), with no distinct isotopic fingerprinting of the dominant source(s). epsilon-Nd values were most valuable for discerning detrital source provenance, and their values at all sites, ranging from ~5.46 to ~3.25, were more unradiogenic for sediments deposited during the last glacial than for those deposited during the Holocene. There are distinct latitudinal trends in the epsilon-Nd values, with more radiogenic values further south and less radiogenic values further north, excluding site 848. This distinction holds true for both Holocene and last glacial periods. For the most southerly site, 848, we invoke, for the first time, a distinct southern hemisphere Australian source as being responsible for the unradiogenic Nd isotope ratios. Both average last glacial and Holocene epsilon-Nd values show similar sharp gradients along the transect between 5.29°N and 2.77°N, suggesting little movement of the glacial ITCZ in the EEP. However, during the deglacial, this gradient is stronger and shifted further north between 5.29°N and 7.21°N, suggesting a more northerly, possibly stronger, deglacial ITCZ.