ALBERT

Description: We investigated the impact of kelp deposition on the geochemistry and microbial community composition of beach sands on the island of Helgoland (North Sea). The composition of the microbial community at a beach with regular kelp deposition appeared shaped by this regular input of organic material, as indicated by significantly higher proportions of aerobic degraders, fermenters, and sulfur cycling microorganisms. Rapid degradation of deposited kelp by this community leads to high levels of dissolved organic and inorganic carbon and nutrients, a lower pH and anoxia. Aerobic respiration, fermentation, Fe- and SO42- reduction and methanogenesis were strongly enhanced, with SO42- reduction being the main process in kelp degradation. SO42- reduction rates increased 20 to 25-fold upon addition of kelp. The main route of electrons from kelp to SO42- was not via CO and H2, as expected, but via organic fermentation products. O2 supply by the tides was not sufficient and reduced intermediates escaped from the sediment with tidal water retraction. The resulting extremely high levels of free sulfide (〉10 mmol L-1) lead to abundant filamentous growth of sulfur-oxidizing bacteria largely composed of a rare O2-adapted Sulfurovum lacking the expected denitrification genes. Our results show that regular kelp deposition strongly enhances the thermodynamic disequilibrium in the beach sand habitat, leading to a dramatic enhancement of the sulfur cycle.

Description: Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.

Description: The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.

Description: In this study, microbial communities in hydrothermal fluids from four different venting areas (White Flames, Cage Site, Woody and Babylon) within the Menez Gwen hydrothermal field (Mid-Atlantic Ridge) were analyzed. Samples were taken along mixing gradients, including diffuse fluid discharge points, their immediate surroundings, and the buoyant parts of hydrothermal plumes, selected based on visible venting, temperature readings and gas concentrations as indicated by in situ mass spectrometry (ISMS) spectra. High throughput 16S rRNA gene amplicon sequences obtained by Illumina paired-end sequencing using the primer combination Bakt_341F and Bakt_805R were analyzed. Total cell counts were determined and fluorescence in situ hybridization was conducted using probes specific for Archaea and Bacteria as well as for different bacterial subgroups. Additionally, three metagenomes were sequenced (Illumina MiSeq paired-end shotgun), assembled, binned, compared and analyzed for key metabolic pathways. Molecular analyses were combined with geochemical analyses and thermodynamic calculations. The study revealed that close to diffuse venting orifices dominated by chemolithoautotrophic Epsilonproteobacteria, in areas where environmental conditions still supported chemolithoautotrophic processes, microbial communities enriched for versatile heterotrophic Alpha- and Gammaproteobacteria were present. The potential for alkane degradation could be shown for several genera and yet uncultured clades. It was proposed that hotspots of chemolithoautotrophic life support a "belt" of heterotrophic bacteria significantly different from the dominating oligotrophic microbiota of the deep sea.

Description: In this dataset, seven inactive massive sulfide chimneys, collected in the Manus Basin (Bismarck Sea, Papua New Guinea, SW Pacific) during SONNE cruise SO216 in 2011, are characterized with respect to mineralogical and geochemical composition as well as age. The samples originate from the PACManus (Snowcap, Fenway, Satanic Mills, Solwara 6, Solwara 8) and SuSu Knolls (North Su) hydrothermal vent fields that emit highly sulfidic fluids and feature poly-metallic sulfide chimneys and mounds. They were collected by the ROV QUEST (Marum Bremen) with the ROV's hydraulic arm. Ore petrology was performed on polished thin sections and shows that the chimneys were mainly composed of chalcopyrite (CuFeS₂), pyrite/marcasite (FeS₂), sphalerite (Zn(Fe)S), and bornite (Cu₅FeS₄) with a suite of other minor to rare minerals. The bulk geochemistry of the samples was determined on representative samples (several tens to hundreds of grams) by a combination of methods including ICP-OES, ICP-MS and Instrumental Neutron Activation. Some samples show elevated As-and Pb-concentrations (up to 3.2 wt.% As; up to 2.0 wt.% Pb), which is also reflected in the presence of tennantite and galena as well as other sulfosalts in thin sections. Five of the seven collected inactive chimney samples were dated using the ²²⁶Ra/Ba method. The youngest, yet clearly inactive sample was StM-R2 (Satanic Mills; 0 y ± 160 y) followed by Fw-R1 (Fenway; 1400 y ± 160 y), Sol8-R1 (Solwara 8; 1800 y ± 160 y) and Sol6-R1 (Solwara 6; 2093 y ± 267 y). The oldest dated chimney was NSu-R7 (North Su; 3183 y ± 236 y). The chimney samples were part of a study, in which 16S rRNA gene based community profiling of active (n=6) and inactive (n=7) sulfide chimneys from the Manus Basin (SW Pacific) was conducted. The diversity information in combination with radiometric dating was used to select a subset of inactive sulfide chimneys of different age for functional analyses on metagenomic (n=4) and metaproteomic (n=1) level.

Description: Thirtythree diffuse fluid and water column samples and 23 samples from surfaces of chimneys, rocks and fauna were subjected to a combined analyses of 16S rRNA gene sequences, metagenomes and real-time in situ measured geochemical parameters to study distribution and niche-partitioning of sulfur-oxidizing bacteria (SOB) in deep-sea hydrothermal environments of the Manus Basin, a back-arc fast-spreading center located between New Britain and New Ireland in the Bismarck Sea. High throughput 16S rRNA gene amplicon sequences obtained by Illumina paired-end sequencing using the primer combination Bakt_341F and Bakt_805R for all samples were analyzed as well as full-length 16S rRNA genes using a Pacific Biosciences RSII sequencer. Additionally, 5 metagenomes were sequenced (Illumina HiSeq 2500, paired-end shotgun), assembled, binned, and re-binned, resulting in 11 Sulfurovum-related, 5 Sulfurimonas-related and 12 SUP05-clade bins. These bins were analyzed with respect to genomic variability among hydrothermal vent SOB and especially with respect to the differentiation of their sulfur oxidation genes. Correlating distribution patterns to real-time geochemical data, tentative niches could be assigned to key hydrothermal SOB clades: Sulfurovum Epsilonproteobacteria were mainly found attached to surfaces exposed to diffuse venting, while the SUP05-clade dominated the bacterioplankton in highly diluted mixtures of vent fluids and seawater. The high diversity within Sulfurimonas- and Sulfurovum-related Epsilonproteobacteria observed in this study was proposed to be derived from the high variation of environmental parameters such as oxygen and sulfide concentrations across small spatial and temporal scales.