ALBERT

Description: The phylogenetic relationship of sulphur-oxidising endosymbiotic bacteria from bivalves of the families Vesicomyidae (Calyptogena sp. C1, Calyptogena sp. C3), Solemyidae (Acharax sp.) and Thyasiridae (Conchocele sp.) from cold-seep habitats were determined by 16S rDNA nucleotide sequence analyses. The endosymbiotic bacteria form distinct groups within the gamma-Proteobacteria and are well separated from each other and from free-living sulphur-oxidising bacteria of the genera Beggiatoa, Halothiobacillus and Thiomicrospira. The endosymbiotic bacteria of Acharax sp. from cold seeps off Oregon, Indonesia and Pakistan have sequences highly similar to each other but quite distinct from other thiotrophic endosymbionts. This includes endosymbionts from Solemya spp., to which they are distantly related. Symbiotic bacteria of Conchocele sp. from a cold seep in the Sea of Okhotsk are similar to those of Bathymodiolus thermophilus and related species, as shown by their overall sequence similarity and by signature sequences. The endosymbiotic bacteria of Calyptogena spp. from cold seeps off Oregon and Pakistan are closely related to those of other vesicomyids. Endosymbiont species found off Oregon corresponded to 2 different clusters of Calyptogena spp. symbionts in the same samples. The results corroborate the hypothesis of a monophyletic origin of the symbionts in vesicomyid clams, and support the existence of deeply branching groups in solemyid symbionts and of divergent lines and distribution for thyasirid symbionts. The results also indicate that certain symbiont species cluster according to the depth distribution of their hosts, and that in consequence host species together with their symbionts may have undergone depth-specific adaptation and evolution.

Description: The Arctic is warming 2–3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.

Description: At Hydrate Ridge (HR), Cascadia convergent margin, surface sediments contain massive gas hydrates formed from methane that ascends together with fluids along faults from deeper reservoirs. Anaerobic oxidation of methane (AOM), mediated by a microbial consortium of archaea and sulfate-reducing bacteria, generates high concentrations of hydrogen sulfide in the surface sediments. The production of sulfide supports chemosynthetic communities that gain energy from sulfide oxidation. Depending on fluid flow, the surface communities are dominated either by the filamentous sulfur bacteria Beggiatoa (high advective flow), the clam Calyptogena (low advective flow), or the bivalve Acharax (diffusive flow). We analyzed surface sediments (0 to 10 cm) populated by chemosynthetic communities for AOM, sulfate reduction (SR) and the distribution of the microbial consortium mediating AOM. Highest AOM rates were found at the Beggiatoa field with an average rate of 99 mmol m-2 d-1 integrated over 0 to 10 cm. These rates are among the highest AOM rates ever observed in methane-bearing marine sediments. At the Calyptogena field, AOM rates were lower (56 mmol m-2 d-1). At the Acharax field, methane oxidation was extremely low (2.1 mmol m-2 d-1) and was probably due to aerobic methane oxidation. SR was fueled largely by methane at flow-impacted sites, but exceeded AOM in some cases, most likely due to sediment heterogeneity. At the Acharax field, SR was decoupled from methane oxidation and showed low activity. Aggregates of the AOM consortium were abundant at the fluid-impacted sites (between 5.1 × 1012 and 7.9 × 1012 aggregates m-2) but showed low numbers at the Acharax field (0.4 × 1012 aggregates m-2). A transport-reaction model was applied to estimate AOM at Beggiatoa fields. The model agreed with the measured depth integrated AOM rates and the vertical distribution. AOM represents an important methane sink in the surface sediments of HR, consuming between 50 and 100% of the methane transported by advection.

Description: Deep-sea whale falls create sulfidic habits Supporting chemoautotrophic communities, but microbial processes underlying the formation Of Such habitats remain poorly evaluated. Microbial degradation processes (sulfate reduction, methanogenesis) and biogeochemical gradients were studied in a whale-fall habitat created by a 30 t whale carcass deployed at 1675 m depth for 6 to 7 yr on the California margin. A variety of measurements were conducted including photomosaicking, microsensor measurements, radio-tracer incubations and geochemical analyses. Sediments were Studied at different distances (0 to 9 in) from the whale fall. Highest microbial activities and steepest vertical geochemical gradients were found within 0.5 m of the whale fall, revealing ex situ sulfate reduction and in vitro methanogenesis rates of up to 717 and 99 mmol m(-2) d(-1), respectively. In sediments containing whale biomass, methanogenesis was equivalent to 20 to 30%, of sulfate reduction. During in vitro sediment studies, sulfide and methane were produced within days to weeks after addition of whale biomass, indicating that chemosynthesis is promoted at early stages of the whale fall. Total sulfide production from sediments within 0.5 m of the whale fall was 2.1 +/- 3 and 1.5 +/- 2.1 mol d(-1) in Years 6 and 7, respectively, of which similar to 200 mmol d(-1) were available as free sulfide. Sulfate reduction in bones was much lower, accounting for a total availability of similar to 10 mmol sulfide d(-1). Over periods of at least 7 yr, whale falls can create sulfidic conditions similar to other chemosynthetic habitats Such as cold seeps and hydrothermal vents.

Description: Biodegradable and compostable plastics are getting more attention as the environmental impacts of fossil-fuel-based plastics are revealed. Microbes can consume these plastics and biodegrade them within weeks to months under the proper conditions. The biobased polyhydroxyalkanoate (PHA) polymer family is an attractive alternative due to its physicochemical properties and biodegradability in soil, aquatic, and composting environments. Standard test methods are available for biodegradation that employ either natural inocula or defined communities, the latter being preferred for standardization and comparability. The original marine biodegradation standard test method ASTM D6691 employed such a defined consortium for testing PHA biodegradation. However, the taxonomic composition and metabolic potential of this consortium have never been confirmed using DNA sequencing technologies. To this end, we revived available members of this consortium and determined their phylogenetic placement, genomic sequence content, and metabolic potential. The revived members belonged to the Bacillaceae, Rhodobacteraceae, and Vibrionaceae families. Using a comparative genomics approach, we found all the necessary enzymes for both PHA production and utilization in most of the members. In a clearing-zone assay, three isolates also showed extracellular depolymerase activity. However, we did not find classical PHA depolymerases, but identified two potentially new extracellular depolymerases that resemble triacylglycerol lipases.

Description: The main objective of the present study was to assess the effects of sulfur (S) nutrition on plant growth, overall quality, secondary metabolites, and antibacterial and radical scavenging activities of hydroponically grown lettuce cultivars. Three lettuce cultivars, namely, Pazmanea RZ (green butterhead, V1), Hawking RZ (green multi-leaf lettuce, V2), and Barlach RZ (red multi-leaf, V3) were subjected to two S-treatments in the form of magnesium sulfate (+S) or magnesium chloride (−S). Significant differences were observed under −S treatments, especially among V1 and V2 lettuce cultivars. These responses were reflected in the yield, levels of macro- and micro-nutrients, water-soluble sugars, and free inorganic anions. In comparison with the green cultivars (V1 and V2), the red-V3 cultivar revealed a greater acclimation to S starvation, as evidenced by relative higher plant growth. In contrast, the green cultivars showed higher capabilities in production and superior quality attributes under +S condition. As for secondary metabolites, sixteen compounds (e.g., sesquiterpene lactones, caffeoyl derivatives, caffeic acid hexose, 5-caffeoylquinic acid (5-OCQA), quercetin and luteolin glucoside derivatives) were annotated in all three cultivars with the aid of HPLC-DAD-MS-based untargeted metabolomics. Sesquiterpene lactone lactucin and anthocyanin cyanidin 3-O-galactoside were only detected in V1 and V3 cultivars, respectively. Based on the analyses, the V3 cultivar was the most potent radical scavenger, while V1 and V2 cultivars exhibited antibacterial activity against Staphylococcus aureus in response to S provision. Our study emphasizes the critical role of S nutrition in plant growth, acclimation, and nutritional quality. The judicious-S application can be adopted as a promising antimicrobial prototype for medical applications.

Description: Epibacterial communities on seaweeds are affected by several abiotic factors such as temperature and acidification. Due to global warming, surface seawater temperatures are expected to increase by 0.5–5 °C in the next century. However, how epibacterial communities associated with seaweeds will respond to global warming remains unknown. In this study, we investigated the response of epibacterial communities associated with the invasive Gracilaria vermiculophylla exposed to 3 °C above ambient temperature for 4 months using a benthocosm system in Kiel, Germany, and 16S rRNA gene amplicon sequencing. The results showed that elevated temperature affected the beta-diversity of the epibacterial communities. Some potential seaweed pathogens such as Pseudoalteromonas, Vibrio, Thalassotalea, and Acinetobacter were identified as indicator genera at the elevated temperature level. Thirteen core raw amplicon sequence variants in the elevated temperature group were the same as the populations distributed over a wide geographical range, indicating that these core ASVs may play an important role in the invasive G. vermicullophylla. Overall, this study not only contributes to a better understanding of how epibacterial communities associated with G. vermiculophylla may adapt to ocean warming, but also lays the foundation for further exploration of the interactions between G. vermiculophylla and its epimicrobiota.

Description: Oxygen (O2) deficiency and nutrient concentrations in marine systems are impacting organisms from microbes to higher trophic levels. In coastal and enclosed seas, O2 deficiency is often related to eutrophication and high degradation rates of organic matter. To investigate the impact of O2 concentration on bacterial growth and the turnover of organic matter, we conducted multifactorial batch experiments with natural microbial communities of the central Baltic Sea. Water was collected from suboxic (〈5 µmol L -1) depths in the Gotland Basin during June 2015. Samples were kept for four days under fully oxygenated and low O2 conditions (mean: 34 µmol L-1 O2), with or without nutrient (ammonium, phosphate, nitrate) and labile carbon (glucose) amendments. We measured bacterial abundance, bacterial heterotrophic production, extracellular enzyme rates (leucine-aminopeptidase) and changes in dissolved and particulate organic carbon concentrations. Our results show that the bacterial turnover of organic matter was limited by nutrients under both oxic and low O2 conditions. In nutrient and glucose replete treatments, low O2 concentrations significantly reduced the net uptake of dissolved organic carbon and lead to higher accumulation of more labile dissolved organic matter. Our results therewith suggest that the combined effects of eutrophication and deoxygenation on heterotrophic bacterial activity may potentially favor the accumulation of dissolved organic carbon in the Baltic Sea.

Description: The family Solemyidae represents ancestral protobranch bivalves with the shallow-water genus Solemya and the deep-sea genus Acharax. All known members of this family host symbiotic sulfur-oxidizing bacteria in their gill filaments. Analysis of 18S rRNA gene sequences of Acharax specimens from methane-seeps off Makran (Pakistan), Java (Indonesia), the Aleutian Trench and off the Oregon, Costa Rica, and Peru margins revealed that Solemya spp. and Acharax spp. are well-separated genetically. This supports the current systematic distinction based on morphological criteria. We found 2 clearly distinct clusters within the genus Acharax, with specimens from the Makran, Oregon and Peru (MOP) margins in one (MOP–Acharax) cluster, and those from Java, the Aleutian Trench and Costa Rica (JAC) in the other (JAC–Acharax) cluster. The separation of MOP– and JAC–Acharax clusters from each other and from Solemya (S. reidi and S. velum) is well-supported by phylogenetic calculations employing maximum likelihood and maximum parsimony. Compared to genetic distances among other protobranch groups, distances between the MOP– and JAC–Acharax clusters would justify the affiliation of these clusters to separate species. This implies that species differentiation in Acharax based on shell morphology is likely to underestimate true species diversity within this taxon. Furthermore, our results support the hypothesis that genetic separation of Solemya and Acharax is congruent with the phylogeny of their bacterial endosymbionts.

Description: Ocean acidification (OA) has provoked changes in the carbonate saturation state that may alter the formation and structural biomineralisation of calcium carbonate exoskeletons for marine organisms. Biomineral production in organisms such as cold-water corals (CWC) rely on available carbonate in the water column and the ability of the organism to sequester ions from seawater or nutrients for the formation and growth of a skeletal structure. As an important habitat structuring species, it is essential to examine the impact that anthropogenic stressors (i.e., OA and rising seawater temperatures) have on living corals and the structural properties of dead coral skeletons; these are important contributors to the entire reef structure and the stability of CWC mounds. In this study, dead coral skeletons in seawater were exposed to various levels of pCO2 and different temperatures over a 12-month period. Nanoindentation was subsequently conducted to assess the structural properties of coral samples’ elasticity (E) and hardness (H), whereas the amount of dissolution was assessed through scanning electron microscopy. Overall, CWC samples exposed to elevated pCO2 and temperature show changes in properties which leave them more susceptible to breakage and may in turn negatively impact the formation and stability of CWC mound development.