Biodegradability of hydrothermally altered deep-sea dissolved organic matter

Deep-sea dissolved organic matter (DOM) constitutes a huge carbon reservoir in the worlds' oceans that – despite its abundance – is virtually unused as a substrate by marine heterotrophs. Heating within hydrothermal systems induces major molecular modifications of deep-sea DOM. Here, we tested the hypothesis that hydrothermal heating of deep-sea DOM enhances bioavailability. Aliquots of DOM extracted from the deep North Pacific (North Equatorial Pacific Intermediate Water; NEqPIW) were re-dissolved in artificial seawater and subjected to temperatures of 100 and 200 °C (40 MPa) using Dickson-type reactors. In agreement with earlier findings we observed a temperature-related drop in dissolved organic carbon (DOC) concentration (−6.1% at 100 °C, −21.0% at 200 °C) that predominantly affected the solid-phase extractable (SPE-DOC) fraction (−18.2% at 100 °C, −51.4% at 200 °C). Fourier-transform ion cyclotron resonance mass spectrometric (FT-ICR-MS) analysis confirmed a temperature-related reduction of average molecular mass, O/C ratios, double bond equivalents (DBE) and a relative increase in aromaticity (AImod). This thermally altered DOM was added (25 μmol L−1 DOC) to deep-water samples from the South West Pacific (Kermadec Arc, RV Sonne / SO253, 32° 37.706′ S | 179° 38.728′ W) and incubated with the prevailing natural microbial community. After 16 days at 4 °C in the dark, prokaryotic cell counts in incubations containing the full spectrum of thermally-degraded DOM (extractable and non-extractable compounds) had increased considerably (on average 21× for DOM100°C and 27× for DOM200°C). In contrast, prokaryotic growth in incubations to which only solid-phase extractable thermally-altered DOM was added was not enhanced compared to control incubations. The experiments demonstrate that temperature-driven degradation of deep-sea recalcitrant DOM within hydrothermal systems turns fractions of it accessible to microbes. The thermally-produced DOM compounds that stimulate microbial growth are not retained on reversed-phase resins (SPE-DOM) and are likely low-molecular mass organic acids. Despite the comprehensive compositional modifications of the solid-phase extractable (SPE-DOM) fraction through heating, it remains inaccessible to microbes at the investigated concentration levels. The microbial incubation resulted in only minor and mostly insignificant overall changes in SPE-DOM molecular composition and concentration

Overlooked Diversity of Ultramicrobacterial Minorities at the Air-Sea Interface

Members of the Candidate phylum Patescibacteria, also called Candidate Phyla Radiation (CPR), are described as ultramicrobacteria with limited metabolic capacities. Wide diversity and relative abundances up to 80% in anaerobic habitats, e.g., in groundwater or sediments are characteristic for Candidatus Patescibacteria. However, only few studies exist for marine surface water. Here, we report the presence of 40 patescibacterial candidate clades at air-sea interfaces, including the upper water layer, floating foams and the sea-surface microlayer (SML), a < 1 mm layer at the boundary between ocean and atmosphere. Particle-associated (>3 μm) and free-living (3–0.2 μm) samples were obtained from the Jade Bay, North Sea, and 16S rRNA (gene) amplicons were analyzed. Although the abundance of Cand. Patescibacteria representatives were relatively low (<1.3%), members of Cand. Kaiserbacteria and Cand. Gracilibacteria were found in all samples. This suggests profound aerotolerant capacities of these phylogenetic lineages at the air-sea interface. The presence of ultramicrobacteria in the >3 μm fraction implies adhesion to bigger aggregates, potentially in anoxic niches, and a symbiotic lifestyle. Due to their small sizes, Cand. Patescibacteria likely become aerosolized to the atmosphere and dispersed to land with possible implications for affecting microbial communities and associated processes in these ecosystems.J.R.: C.S., O.W. and this study were funded by the European Research Council project PASSME, grant number GA336408. The picture of seafoam was taken during a campaign funded by the Assemble Plus project MIDSEAS (European Union’s Horizon 2020 research and innovation program, Grant Agreement No. 730984). D.P.R.H. was supported by the European Regional Development Fund/Estonian Research Council funded by “Mobilitas Plus Top Researcher grant MOBTT24”. A.J.P. received funding by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen (“Nachwuchsgruppe Alexander Probst”). The APC was funded by the Open Access Publication Fund of the University of Duisburg-Essen.J.R.: C.S., O.W. and this study were funded by the European Research Council project PASSME, grant number GA336408. The picture of seafoam was taken during a campaign funded by the Assemble Plus project MIDSEAS (European Union’s Horizon 2020 research and innovation program, Grant Agreement No. 730984). D.P.R.H. was supported by the European Regional Development Fund/Estonian Research Council funded by “Mobilitas Plus Top Researcher grant MOBTT24”. A.J.P. received funding by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen (“Nachwuchsgruppe Alexander Probst”). The APC was funded by the Open Access Publication Fund of the University of Duisburg-Essen

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

Oxygen Profiles Across the Sea-Surface Microlayer—Effects of Diffusion and Biological Activity

Gas exchange across the air-water interface is strongly influenced by the uppermost water layer (&lt; 1 mm), the sea-surface microlayer (SML). However, a clear understanding about how the distinct physicochemical and biological properties of the SML affect gas exchange is lacking. We used an automatic microprofiler with Clark-type microsensors to measure small-scale profiles of dissolved oxygen in the upper 5 cm of the water column in a laboratory tank filled with natural seawater. We aimed to link changing oxygen concentrations and profiles with the metabolic activity of plankton and neuston, i.e., SML-dwelling organisms, in our artificial, low-turbulence set-up during diel cycles. We observed that temporal changes of the oxygen concentration in near surface water (5 cm depth) could not be explained by diffusive loss of oxygen, but by planktonic activity. Interestingly, no influence of strong neuston activity on oxygen gradients at the air-water interface was detectable. This could be confirmed by a modeling approach, which revealed that neuston metabolic activity was insufficient to create distinct curvatures into these oxygen gradients. Moreover, the high neuston activity in our study contributed only ≤ 7.1% (see Supplementary Table 4) to changes in oxygen concentration in the tank. Overall, this work shows that temporal and vertical variation of oxygen profiles across the air-water interface in controlled laboratory set-ups is driven by biological processes in the underlying bulk water, with negligible effects of neuston activity

Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation

The marine roseobacter-clade affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodeling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), RCA bacteria synthesize a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation

Master track of HEINCKE cruise HE571 in 1 sec resolution (zipped, 2.6 MB)

Raw data acquired by position sensors on board RV Heincke during expedition HE571 were processed to receive a validated master track which can be used as reference of further expedition data. During HE571 the inertial navigation system IXSEA PHINS III and the GPS receivers Trimble Marine SPS461 and SAAB R5 SUPREME NAV were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report found at EPIC repository https://hdl.handle.net/10013/epic.9e97197f-615a-4b7e-ae0f-80ced2d10e0e. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track

Master track of HEINCKE cruise HE615 in 1 sec resolution (zipped, 2.4 MB)

Raw data acquired by position sensors on board RV Heincke during expedition HE615 were processed to receive a validated master track which can be used as reference of further expedition data. During HE615 the inertial navigation system IXSEA PHINS III and the GPS receivers Trimble Marine SPS461 and SAAB R5 SUPREME NAV were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.awi.de) with a resolution of 1 sec. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track