The Role of Cu-oxide and Cu adatoms in the Reactivity of CO2 on Cu(110).

We investigate the interaction of CO2 with metallic and oxidized Cu(110) surfaces using a combination of near-ambient pressure scanning tunneling microscopy (NAP-STM) and theory calculations. While the Cu(110) and full CuO films are inert, the interface between bare Cu(110) and the CuO film is observed to react instantly with CO2 at a 10 mbar pressure. The reaction is observed to proceed from the interfacial sites of CuO/Cu(110). During reaction with CO2, the CuO/Cu(110) interface releases Cu adatoms which combine with CO3 to produce a variety of added Cu-CO3 structures, whose stability depends on the gas pressure of CO2. A main implication for the reactivity of Cu(110) is that Cu adatoms and highly undercoordinated CuO segments are created on the Cu(110) surface through the interaction with CO2, which may act as reaction-induced active sites. In the case of CO2 hydrogenation to methanol, we used theory to assess such sites to indicate that their presence may significantly promote CH3OH formation. Our study thus implies that the CuO/Cu(110) interfacial system is highly dynamic in the presence of CO2, and it suggests a possible strong importance of reaction-induced Cu and CuO sites for the surface chemistry of Cu(110) in CO2-related catalysis.

Visualizing the gas-sensitive structure of the CuZn surface in methanol synthesis catalysis.

Methanol formation over Cu/ZnO catalysts is linked with a catalytically active phase created by contact between Cu nanoparticles and Zn species whose chemical and structural state depends on reaction conditions. Herein, we use variable-temperature scanning tunneling microscopy at elevated pressure conditions combined with X-ray photoelectron spectroscopy measurements to investigate the surface structures and chemical states that evolve when a CuZn/Cu(111) surface alloy is exposed to reaction gas mixtures. In CO2 hydrogenation conditions, Zn stays embedded in the CuZn surface, but once CO gas is added to the mixture, the Zn segregates onto the Cu surface. The Zn segregation is CO-induced, and establishes a new dynamic state of the catalyst surface where Zn is continually exchanged at the Cu surface. Candidates for the migrating few-atom Zn clusters are further identified in time-resolved imaging series. The findings point to a significant role of CO affecting the distribution of Zn in the multiphasic ZnO/CuZn/Cu catalysts.

An approach for patterned molecular adsorption on ferromagnets, achieved via Moiré superstructures.

We have used a scanning tunneling microscope operated under ultrahigh vacuum conditions to investigate an oxo-vanadium-salen complex V(O)salen, that has potential applications as qubits in future quantum-based technologies. The adsorption and self-assembly of V(O)salen on a range of single crystal metal surfaces and nanoislands and the influence of substrate morphology and reactivity has been measured. On the close-packed flat Ag(111) and Cu(111) surfaces, the molecules adsorb isolated or form small clusters arranged randomly on the surface, whereas structured adsorption occurs on two types of Co nanoislands; Co grown on Ag(111) and Ag capped Co islands grown on Cu(111), both forming a Moiré pattern at the surface. The adsorption configuration can by scanning tunneling spectroscopy be linked to the geometric and electronic properties of the substrates and traced back to a Co d-related surface state, illustrating how the modulated reactivity can be used to engineer a pattern of adsorbed molecules on the nanoscale.

Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands.

Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2  h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.

Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation.

Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae 'Candidatus Acestibacter aggregatus' that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.

Diversity of deep-water coral-associated bacteria and comparison across depth gradients.

Environmental conditions influence species composition, including the microbial communities that associate with benthic organisms such as corals. In this study we identified and compared bacteria that associate with three common deep-water corals, Lophelia pertusa, Madrepora oculata and Paragorgia arborea, from a reef habitat on the mid-Norwegian shelf. The 16S rRNA gene amplicon sequencing data obtained revealed that >50% of sequences were represented by only five operational taxonomic units. Three were host-specific and unclassified below class level, belonging to Alphaproteobacteria with affiliation to members of the Rhizobiales order (L. pertusa), Flavobacteria affiliated with members of the Elisabethkingia genus (M. oculata) and Mollicutes sequences affiliated with the Mycoplasma genus (P. arborea). In addition, gammaproteobacterial sequences within the genera Sulfitobacter and Oleispira were found across all three deep-water coral taxa. Although highly abundant in the coral microbiomes, these sequences accounted for <0.1% of the surrounding bacterioplankton, supporting specific relationships. We combined this information with previous studies, undertaking a meta-data analysis of 165 widespread samples across coral hosts and habitats. Patterns in bacterial diversity indicated enrichment of distinct uncultured species in coral microbiomes that differed among deep (>200 m), mesophotic (30-200 m) and shallow (<30 m) reefs.

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle.

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities.

Deep-sea coral reefs do not receive sunlight and depend on plankton. Little is known about the plankton composition at such reefs, even though they constitute habitats for many invertebrates and fish. We investigated plankton communities from three reefs at 260-350 m depth at hydrocarbon fields off the mid-Norwegian coast using a combination of cultivation and small subunit (SSU) rRNA gene and transcript sequencing. Eight months incubations of a reef water sample with minimal medium, supplemented with carbon dioxide and gaseous alkanes at in situ-like conditions, enabled isolation of mostly Alphaproteobacteria (Sulfitobacter, Loktanella), Gammaproteobacteria (Colwellia) and Flavobacteria (Polaribacter). The relative abundance of isolates in the original sample ranged from ∼ 0.01% to 0.80%. Comparisons of bacterial SSU sequences from filtered plankton of reef and non-reef control samples indicated high abundance and metabolic activity of primarily Alphaproteobacteria (SAR11 Ia), Gammaproteobacteria (ARCTIC96BD-19), but also of Deltaproteobacteria (Nitrospina, SAR324). Eukaryote SSU sequences indicated metabolically active microalgae and animals, including codfish, at the reef sites. The plankton community composition varied between reefs and differed between DNA and RNA assessments. Over 5000 operational taxonomic units were detected, some indicators of reef sites (e.g. Flavobacteria, Cercozoa, Demospongiae) and some more active at reef sites (e.g. Gammaproteobacteria, Ciliophora, Copepoda).

High diversity of microplankton surrounds deep-water coral reef in the Norwegian Sea.

Coral reefs that exist in the depths of the oceans are surrounded by Eukarya, Archaea and bacterial communities that may play an important role in the nutrition and health of the reef. The first interdomain community structure of planktonic organisms in seawater from a deep-water coral reef is described. Community profiling and analysis of ribosomal RNA gene sequences from a coral reef system at 350 m depth in the Norwegian Sea revealed a rich diversity of Eukarya and Bacteria and a moderate diversity of Archaea. Most sequences affiliated with marine microplankton from deep-sea to cold-surface regions, with many sequences being similar to those described in studies of mesopelagic and oxygen minimum zones. Dominant phylotypes belonged to the Alveolata (group I, II, dinoflagellates), Stramenopiles (silicoflagellates), Alphaproteobacteria (Pelagibacter ubique), Gammaproteobacteria (ARCTIC96BD-19), Bacteroidetes (Flavobacteria) and mesophilic Crenarchaeota (Nitrosopumilus maritimus). Several rare and novel members of the community fell into distinct phylogenetic groups. The inferred function of dominant community members suggested autotrophs that utilise light, ammonium or sulphide, and lifestyles based on host associations. The high diversity reflected a microplankton community structure, which is significantly different from that of microplankton collected at the same depth at a pelagic station away from reefs.

Differential expression of particulate methane monooxygenase genes in the verrucomicrobial methanotroph 'Methylacidiphilum kamchatkense' Kam1.

Methane monooxygenases (MMOs) are oxygen-dependent enzymes that catalyze the oxidation of methane to methanol in the methanotrophic bacteria. The thermoacidophilic verrucomicrobial methanotroph 'Methylacidiphilum kamchatkense' Kam1 contains three complete and phylogenetically distinct copies of the pmoCAB gene cluster apparently organized as operons, each encoding all three subunits of particulate MMO (pMMO), and a truncated pmoCA cluster encoding only two of the subunits. Two of the clusters are present as a tandem array, but the other clusters occur in isolation. Here, the expression of these clusters has been assessed using the four pmoA genes as targets in reverse transcriptase quantitative PCR analysis. One of the pmoA genes, designated pmoA2, is at least 35-fold more strongly transcribed than the other pmoA copies. Growth at suboptimal temperature and pH conditions did not significantly change the transcription pattern, indicating that the pmoCAB2 cluster encodes the functional pMMO under methane-fuelled growth conditions. During growth on methanol, expression of pmoA2 was reduced approximately tenfold as compared to growth on methane, suggesting a role for the alternative carbon substrates in gene regulation.

Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms.

Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (T (opt)) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that T (opt) evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.

Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves.

A novel bacterium was discovered in the gills of the large bivalve Acesta excavata (Limidae) from coral reefs on the northeast Atlantic margin near the shelf break of the fishing ground Haltenbanken of Norway, and confirmed present in A. excavata from a rock-wall in the Trondheimsfjord. Purified gill DNA contained one dominant bacterial rRNA operon as indicated from analysis of broad range bacterial PCR amplicons in denaturant gradient gels, in clone libraries and by direct sequencing. The sequences originated from an unknown member of the order Oceanospirillales and its 16S rRNA gene fell within a clade of strictly marine invertebrate-associated Gammaproteobacteria. Visual inspection by fluorescent in situ hybridization and transmission electron microscopy indicated a pleomorphic bacterium with no visible cell wall, located in aggregates inside vacuoles scattered within the gill cells cytoplasm. Intracellular Oceanospirillales exist in bathymodiolin mussels (parasites), Osedax worms and whiteflies (symbionts). This bacterium apparently lives in a specific association with the Acesta.

The nonrandom microheterogeneity of 16S rRNA genes in Vibrio splendidus may reflect adaptation to versatile lifestyles.

16S rRNA molecules in a microbial strain can differ due to nucleotide variation between their genes. This is a typical trait of fast-growing bacteria to cope with different niches. We investigated characteristics of 16S rRNA genes in Vibrio splendidus strain PB1-10, from the normal flora of Atlantic halibut. Sequencing of 16S rRNA gene clones detected 35 variable positions in a total of 13 different gene copies. More than two-thirds of the substitutions occurred in regions corresponding to helix H6 and helix H17 of the 16S rRNA molecule. Possible recombination between these helixes in related bacteria (Vibrio, Photobacterium, Colwellia) from similar environments impacts 16S rRNA-based phylogeny of V. splendidus. We argue that these nonrandom modifications are maintained to provide a fine-tuning of the ribosome function to optimize translation machinery performance and ultimately bacterial niche fitness.

Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of Norway.

Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 micromol 13CH4 g(-1) wet weight occurred. Extracted DNA was separated into 'light' and 'heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs.

Methane oxidation at 55 degrees C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum.

Methanotrophic bacteria constitute a ubiquitous group of microorganisms playing an important role in the biogeochemical carbon cycle and in control of global warming through natural reduction of methane emission. These bacteria share the unique ability of using methane as a sole carbon and energy source and have been found in a great variety of habitats. Phylogenetically, known methanotrophs constitute a rather limited group and have so far only been affiliated with the Proteobacteria. Here, we report the isolation and initial characterization of a nonproteobacterial obligately methanotrophic bacterium. The isolate, designated Kam1, was recovered from an acidic hot spring in Kamchatka, Russia, and is more thermoacidophilic than any other known methanotroph, with optimal growth at approximately 55 degrees C and pH 3.5. Kam1 is only distantly related to all previously known methanotrophs and belongs to the Verrucomicrobia lineage of evolution. Genes for methane monooxygenases, essential for initiation of methane oxidation, could not be detected by using standard primers in PCR amplification and Southern blot analysis, suggesting the presence of a different methane oxidation enzyme. Kam1 also lacks the well developed intracellular membrane systems typical for other methanotrophs. The isolate represents a previously unrecognized biological methane sink, and, due to its unusual phylogenetic affiliation, it will shed important light on the origin, evolution, and diversity of biological methane oxidation and on the adaptation of this process to extreme habitats. Furthermore, Kam1 will add to our knowledge of the metabolic traits and biogeochemical roles of the widespread but poorly understood Verrucomicrobia phylum.

Phylogenetic analysis of bacterial communities associated with larvae of the Atlantic halibut propose succession from a uniform normal flora.

Halibut, the largest of all flatfishes is a valuable species with a great potential for aquaculture. Bacteria play an important role in regulating the health of the early life stages. The present article is the first broad-range molecular analysis of bacterial communities in larvae of the Atlantic halibut (Hippoglossus hippoglossus). DNA was extracted from larvae, water and silo biofilm from hatcheries in Norway, Scotland, Iceland and Canada. Eubacterial 16S rRNA gene fragments were amplified by polymerase chain reaction (PCR) with broad-range primers. Sequences spanning the hyper variable V3 region representing individual bacterial species were separated into community profiles by denaturing gradient gel electrophoresis (DGGE). The profiles revealed simple communities after hatching and bacterial succession following growth. Sequencing and phylogenetic analysis of excised DGGE bands suggested aerobic heterotrophs related to groups of Pseudomonas, Janthinobacterium and possibly Marinomonas to be the primary colonisers of the larvae. After onset of feeding, fermentative species (Vibrio) were detected as well. Comparative analysis of bacterial communities from different geographical regions indicated that larvae of the Atlantic halibut possess a distinct and specific normal flora.

Selection and identification of autochthonous potential probiotic bacteria from turbot larvae (Scophthalmus maximus) rearing units.

The purpose of this study was to select, identify and characterise bacteria as a disease control measure in the rearing of marine fish larvae (turbot, Scophthalmus maximus). Thirty-four out of 400 marine bacterial strains exhibited in vitro anti-bacterial activity against three fish larval pathogens. Two strains originated from culture collections and thirty two strains were isolated directly from turbot larvae rearing units using a pre-selection procedure to facilitate detection of antagonists. Approximately 8,500 colonies from colony-count plates were replica-plated on agar seeded with Vibrio anguillarum, and 196 of them caused zones of clearing in the V. anguillarum agar layer. Of these, 32 strains exhibited reproducible antibacterial properties in vitro when tested against the fish pathogens V. anguillarum 90-11-287, V. splendidus DMC-1 and a Pseudoalteromonas HQ. Seventeen antagonists were identified as Vibrio spp. and four of twelve tested were lethal to yolk-sac larvae. The 15 remaining strains were identified as Roseobacter spp. based on phenotypic criteria and 16S rDNA gene sequence analysis of two strains representing the two major RAPD groups. Most of the remaining 164 strains selected in the initial replica plating were identified as Vibrionaceae or Pseudoalteromonas. Roseobacter spp. were not lethal to egg yolk sac turbot larvae and in two of three trials, the mortality of larvae decreased (p > 0.001) in treatments where 10(7) cfu/ml Roseobacter sp. strain 27-4 was added, indicating a probiotic potential.

Characterization of strains of Vibrio splendidus and V. tapetis isolated from corkwing wrasse Symphodus melops suffering vibriosis.

Two vibrio bacteria pathogenic to the corkwing wrasse Symphodus melops were isolated. Vibriosis-inducing strain LP1 was isolated as the dominanting bacterium in kidney samples of dead and moribund wrasse from a population suffering vibriosis and high daily mortality in 1998 on the Norwegian west coast. The other vibriosis-inducing strain, LP2, was isolated from wrasse captured the following year. Re-infection experiments have confirmed that these strains cause vibriosis in corkwing wrasse. Both strains were typical vibrios sharing the traits of fermentative Gram-negative curved rods with motility and a positive oxidase reaction. Detailed biochemical and genetic characterisation revealed a close affiliation to known species of the marine environment. The first isolate, LP1, is a form of the ubiquitous seawater organism Vibrio splendidus, while the second isolate, LP2, is closely related to V. tapetis (previously only known as the brown ring disease agent in clams). Identification of the new wrasse pathogens V. splendidus LP1 and V. tapetis LP2 is facilitated by break points observed in this study.

Use of PCR-RFLP for genotyping 16S rRNA and characterizing bacteria cultured from halibut fry.

Small subunit ribosomal genes were explored using PCR-RFLP to facilitate the characterization of bacteria cultured from reared fry of the Atlantic halibut (Hippoglossus hippoglossus). Concern has been expressed about pathogen invasion in larvae lacking a counteracting normal flora that may aid the immune system in producing robust noninfected individuals. In this study, pure cultured representatives of normal flora that were previously found to be antagonistic towards a pathogenic Vibrio sp. were subjected to a whole cell PCR protocol amplifying approximately 1500 bp of 16S rDNA. Amplified DNA was digested by AluI, BstUI, CfoI, and RsaI, to generate restriction profiles. Before the isolates were characterized, a survey was performed to test the discriminative efficiency of the RFLP. Efficient detection of polymorphism and the resolution of species and subspecies were achieved. Using the RFLP on 103 isolates generated as many as 22 genotypes. Based on the restriction profiles, a taxonomic tree incorporating 19 reference strains was constructed. Partial sequencing found this tree to be dominated by gamma-Proteobacteria in clusters of Vibrio-, Pseudomonas-, and Alteromonas-affiliated species. Only nine isolates fell outside these genera, including the three isolates Shewanella alga, Deleya marina, and Marinomonas protea. These species have not previously been reported as halibut flora. The most frequently isolated genotype resembled Vibrio salmonicida.