Charakterisierung Interferon-gamma-induzierter Gene: Interferon-induzierbares Protein 35, Nociceptin/Orphanin FQ und humanes Guanylat-bindendes Protein 3

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Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria).

Assie A, Leisch N, Meier DV, et al. Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). The ISME journal. 2019;14(1):104-122.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 cyclegenes 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

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses

Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitat

Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes

Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analysed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (22% McV; 52% BrV). In each of the three plumes analysed, the community was dominated by a different chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles revealed a SUP05 niche partitioning based on iron availability, sulfide and depth. A fourth SUP05 species was present at low frequencies throughout investigated plume samples and may be capable of a heterotrophic/mixotrophic lifestyle. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes. CARD-FISH analysis was conducted according to Pernthaler et al. (2002; doi:10.1128/AEM.68.6.3094-3101.2002). Cell permeabilization was conducted at 37°C for 60 min with 10 mg/ml lysozyme. Additionally, archaeal cell walls were permeabilized with 15 µg/ml proteinase K for 3 minutes at room temperature. Endogenous peroxidases were inactivated with 0.1 M HCl for 10 min. Counterstaining was done with 1 µg/ml 4',6 diamidino-2-phenylindole (DAP

Anaerobic methanotrophic archaea-2 and Desulfosarcina/Desulfococcus group in sediments at different stations

The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). In sediment samples from Hydrate Ridge, the Isis Mud Volcano and the Gulf of Mexico, DSS cells accounted for 3-6% of all DAPI-stained single cells. Out of these, 8-17% were labelled with probe SEEP1a-1441. This translated into relative abundances of single SEEP-SRB1a cells of 0.3% to 0.7%. Contrastingly, in a sediment sample from the Gullfaks oil field, DSS cells accounted for 18% and SEEP-SRB1a for 9% of all single cells. This sediment sample also featured an unusually high abundance of single ANME-2 cells and only very few ANME-2/DSS aggregates in comparison with other AOM habitats. Considering also the nature of the sample, it is likely that the high number of single ANME-2 and SEEP-SRB1a cells were an artifact of sample preparation. Here, harsher sonication was required to remove the microorganisms from coarse sand prior to CARD-FISH analysis

Metagenomic approach to the study of halophages: The environmental halophage 1

Hypersaline environments, such as crystallizer ponds of solar salterns, show one of the highest concentration of viruses reported for aquatic systems. All the halophages characterized so far are isolates obtained by cultivation from described haloarchaeal species that have only low abundance in the environment. We employed a culture-independent metagenomic approach to analyse for the first time complete genomes in the halophage community and explored the in situ diversity by transmission electron microscopy and pulsed-field gel electrophoresis. We report the genomic sequence of a not yet isolated halophage (named as environmental halophage 1 'EHP-1′) whose DNA was obtained from crystallizer samples with a salinity of 31%. The sequenced genome has a size of 35 kb and a G + C content around 51%. The G + C content is lower than that of previously characterized halophages. However, G + C content and codon usage in EHP-1 are similar to the recently cultivated and sequenced Haloquadratum walsbyi, the major prokaryotic component in solar salterns around the world. Forty open reading frames have been predicted, including genes that putatively code for proteins involved in DNA replication (ribonucleotide reductases, thymidylate kinase) normally found in lytic viruses. © 2007 The Authors.This work was funded by the FP6-EU Network of Excellence Marine Genomics (Contract Nb 505403), the Max Planck Society, the Spanish Ministry of Science and Education Grants BOS2003-05198-C02-01 and -02 and the Generalitat Valenciana (Grant ACOMP06/097)Peer Reviewe

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The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7- 21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur com- ponents. High sulfate reduction rates as well as sulfide depleted in 34S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic- hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen

Clustered Genes Related to Sulfate Respiration in Uncultured Prokaryotes Support the Theory of Their Concomitant Horizontal Transfer

The dissimilatory reduction of sulfate is an ancient metabolic process central to today's biogeochemical cycling of sulfur and carbon in marine sediments. Until now its polyphyletic distribution was most parsimoniously explained by multiple horizontal transfers of single genes rather than by a not-yet-identified “metabolic island.” Here we provide evidence that the horizontal transfer of a gene cluster may indeed be responsible for the patchy distribution of sulfate-reducing prokaryotes (SRP) in the phylogenetic tree. We isolated three DNA fragments (32 to 41 kb) from uncultured, closely related SRP from DNA directly extracted from two distinct marine sediments. Fosmid ws39f7, and partially also fosmids ws7f8 and hr42c9, harbored a core set of essential genes for the dissimilatory reduction of sulfate, including enzymes for the reduction of sulfur intermediates and synthesis of the prosthetic group of the dissimilatory sulfite reductase. Genome comparisons suggest that encoded membrane proteins universally present among SRP are critical for electron transfer to cytoplasmic enzymes. In addition, novel, conserved hypothetical proteins that are likely involved in dissimilatory sulfate reduction were identified. Based on comparative genomics and previously published experimental evidence, a more comprehensive model of dissimilatory sulfate reduction is presented. The observed clustering of genes involved in dissimilatory sulfate reduction has not been previously found. These findings strongly support the hypothesis that genes responsible for dissimilatory sulfate reduction were concomitantly transferred in a single event among prokaryotes. The acquisition of an optimized gene set would enormously facilitate a successful implementation of a novel pathway

Environmental parameters of deep-sea hydrothermal vents from the Manus Basin

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

Mineralogical and geochemical characterisation of iron-sulfur deposits from the Manus Basin (SW Pacific) sampled during SONNE cruise SO216 in 2011

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