1,721,093 research outputs found
Hydrogen uptake activities of metagenomic fosmid clones derived from hydrothermal vent systems along the Mid-Atlantic Ridge during METEOR cruise M78/2
No full textMetagenomic fosmid libraries were constructed from hydrothermal chimneys and fluids and screened for hydrogen uptake (hydrogenase) activity by means of an activity-based screen. The hydrogen uptake activity of positively screened clones was determined by means of a spectrophotometric assay and the DNA-sequences of the respective fosmid inserts were determined by PacBio Sequencing. The dataset contain hydrogen-uptake activities of fosmid clones from the Sisters Peak, Nibelungen and Lilliput hydrothermal vent fields
Influence of flanking genes on Gammaproteobacterial form I and II RubisCO functioning
No full textSince the majority of all microorganisms are currently not culturable, we used a metagenomic approach to identify genes and enzymes associated with RubisCO expression. The investigated metagenomic DNA fragment originates from the deep-sea hydrothermal vent field Nibelungen at 8°18'S along the Mid-Atlantic Ridge. It is 13,023 bp and resembles genes from Thiomicrospira crunogena. The fragment encodes nine open reading frames (ORFs) which include two types of RubisCO, form I (CbbL/S) and form II (CbbM), two LysR transcriptional regulators (LysR1 and LysR2), two von Willebrand factor type A (CbbO-m and CbbO-1), and two AAA+ ATPases (CbbQ-m and CbbQ-1), expected to function as RubisCO activating enzymes. To date, only one study has ever investigated regulatory mechanisms in metagenome-derived RubisCO gene clusters (Böhnke and Perner 2015). Here, total RubisCO activity was significantly influenced when cbbL and cbbM neighboring genes were knocked out (Böhnke and Perner 2015), but it remained unclear which of the two RubisCOs was primarily affected by these mutations. Our study suggests that CbbQ-m and CbbO-m activate CbbL and that LysR1 and LysR2 proteins promote CbbQ-m/CbbO-m expression. CbbO-1 seems to activate CbbM and CbbM itself appears to contribute to intensifying LysR's binding ability and thus its own transcriptional regulation. CbbM furthermore appears to impair cbbL expression
Specific RubisCO activity of currently uncultured microorganisms inhabiting hydrothermal deep sea vents
No full textIn 2014 we described a new activity-based screen suited to seek active recombinant RubisCOs from the environment - independent of the native host's culturability. Within this study we aimed at seeking novel RubisCO active enzymes from the environment. For this purpose we screened six metagenomic fosmid libraries from hydrothermal vent environments, differing with respect to their (i) geographic origin (north or south Mid Atlantic Ridge) and their (ii) environmental characteristics (basalt vs. ultramafic hosted, temperature, and pH). Overall we screened roughly 12500 metagenomic fosmid clones and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted
Specific RubisCO activities of yet uncultured Proteobacteria depending on flanking genes
No full textHere we used the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. Hydrothermal vent fluids derived from the interface zone between hot fluids emanating from Drachenschlund and ambient cold seawater at 8°18'S/13°30'W served as initial sample for library construction. Among 1056 screened fosmid clones 12 exhibited RubisCO activity. The metagenomic fragments of all twelve clones resembled genes from Hydrogenovibrio crunogenus. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of 12 genes and 2 intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly-characterized gene and RubisCO activity
Master track of ELISABETH MANN BORGESE cruise EMB374 in 1 sec resolution (zipped, 40 MB)
No full textRaw data acquired by position sensors on board RV Elisabeth Mann Borgese during expedition EMB374 were processed to receive a validated master track which can be used as reference of further expedition data. During EMB374 data from the motion reference unit exail Phins Gen.3, the Trimble SPS356 GPS receiver, the Furuno GP-170 and the Furuno GP-150 GPS receiver were used to calculate the mastertrack. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. 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 tracks in different resolutions of ELISABETH MANN BORGESE cruise EMB374, Kiel - Rostock, 2025-09-02 - 2025-09-13
No full textRaw data acquired by position sensors on board RV Elisabeth Mann Borgese during expedition EMB374 were processed to receive a validated master track which can be used as reference of further expedition data. During EMB374 data from the motion reference unit exail Phins Gen.3, the Trimble SPS356 GPS receiver, the Furuno GP-170 and the Furuno GP-150 GPS receiver were used to calculate the mastertrack. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. 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
Water column, solid phase and porewater data in the Kiel Bight, SW Baltic Sea from 2016 to 2025
No full textDuring the research cruises BE03/2016 (08.03.2016), BE10/2016 (19.10.2016), BE10/2018 (23.10.2018), BE03/2019 (15.03.2019), L23-13 (13.09.2023 - 15.09.2023), Sagitta24-1 (16.09.2024), Sagitta24-2 (23.09.2024), Hai24VE2 (24.09.2024), L25-2b (09.02.2025 - 17.02.2025) and EMB374 (04.09.2025 - 13.09.2025), CTDs were deployed and sediment corers were retrieved at 99 stations in Kiel Bight in the southwestern Baltic Sea. Water column oxygen concentrations were determined using oxygen sensors attached to the CTD framework. At selected water depths, water samples were collected with Niskin bottles for the analysis of nitrate concentrations using an autoanalyzer. Short sediment cores (<50cm) were recovered using a Multicorer (MUC), Minicorer (MIC) or Rumohrlot (RL). Bottom waters were sampled from the supernatant water in the sediment cores. Solid phase sediment samples were analyzed for total organic carbon using an element analyzer. Porewater was extracted from the sediment cores using rhizones and analyzed for total alkalinity (titration), ammonium (photometer), sulfate (ion chromatography), hydrogen sulfide (photometer), dissolved iron (ICP-OES) and dissolved manganese (ICP-OES). The collected data will be used to (i) determine the spatial and temporal variability of hydrogen sulfide in bottom waters of the Kiel Bight, (ii) identify the controlling factors governing the accumulation of hydrogen sulfide at the seafloor, and (iii) establish an early warning system of sulfidic seafloor conditions for regional stakeholders in the Baltic Sea
Carbon monoxide (CO) and dimethylsulphide (DMS) cycling in a changing arctic ocean
Full text linkThis study examines the relationship between the carbon monoxide (CO) and dimethyl sulphide (DMS) cycles in the surface waters of the Arctic Ocean and their interactions with environmental factors such as ocean acidification, changing light conditions, and abiotic factors. The radiation budget of the atmosphere above the Arctic Ocean plays a crucial role in global climate, and understanding the processes that influence it is important for mitigating the effects of global warming. Climate-relevant gases like CO and DMS can affect the radiation budget in the Arctic atmosphere. However, due to limited information on CO in the Arctic and incomplete knowledge of the processes and interactions related to DMS production, there is uncertainty regarding future CO and DMS production pathways and emissions in this region. Therefore, this study aims to provide insights into the CO and DMS cycle in the Arctic Ocean surface waters and their interactions with environmental factors
Ein neues funktionsbasiertes Screeningverfahren zum Auffinden RubisCO aktiver Klone aus Metagenombanken : Bedeutung RubisCO assoziierter Enzyme.
No full textDas Enzym Ribulose-1,5-bisphosphat Carboxylase/Oxygenase (RubisCO; EC 4.1.1.39) katalysiert die Schlüsselreaktion des Calvin Benson (CB) Zyklus, eine Reaktion bei dem erstmalig im Ablauf des Zyklus Kohlenstoff fixiert wird. Dieses einzigartige Enzym kommt in allen Pflanzen, Cyanobakterien und vielen autotrophen Bakterien vor (phototrophe und chemotrophe Prokaryoten) und fast der gesamte, weltweit durch Primärproduzenten assimilierte anorganische Kohlenstoff kann auf die Aktivität der RubisCO zurückgeführt werden (>99.5%). Die meisten Studien die das Wissen um die Funktionsweise der RubisCO erweitert haben, wurden mit Pflanzen oder kultivierbaren Mikroorganismen durchgeführt. Die Funktionalität von RubisCO Enzymen aus der Umwelt sowie die Bedeutung flankierender Genregionen ist jedoch noch immer ungeklärt. Derzeit gibt es keinen funktionsbasierten Ansatz, der es ermöglicht RubisCO aktive Enzyme direkt aus der Umwelt zu isolieren. Die Mehrheit funktionsfähiger RubisCOs und RubisCO assoziierter Gene unkultivierter Mikroorganismen (>99%) bleibt folglich unzugänglich.
In dieser Studie wird erstmals ein funktionsbasierter Ansatz vorgestellt, der es ermöglicht Metagenombanken nach Klonen mit RubisCO-Aktivität zu durchsuchen und dementsprechend RubisCOs direkt in Umweltproben zu detektieren. Unter Anwendung des neu etablierten Durchmusterungsverfahrens wurden insgesamt zwölf RubisCO aktive Klone identifiziert, die sequenzielle Übereinstimmungen zu Thiomicrospira crunogena aufwiesen. Die 35.2 kb umfassenden metagenomischen DNA Fragmente bestehen aus einem RubisCO Gen Cluster und flankierender DNA. Des Weiteren
wurde die Bedeutung der auf dem metagenomischen DNA Fragment kodierten Genen in Bezug auf die Expression einer voll funktionsfähigen RubisCO analysiert, indem einzelne Gene durch Transposon Insertionen ausgeschalten wurden. Hier wurde unter
anderem ein Gen detektiert (orf06), das für ein hypothetisches Protein kodiert das niemals zuvor mit der Funktionsfähigkeit des RubisCO Enzyms in Verbindung gebracht wurde, jedoch direkt oder indirekt die Transkription sowohl von cbbL als auch von
cbbM aktivierend reguliert. Signifikant veränderte RubisCO Aktivitäten wurden darüber hinaus für elf weitere ausgeschaltene Gene gemessen, die entweder für Proteine kodieren die als transkriptionelle Regulatoren annotiert sind oder für Proteine von den angenommen wird, dass sie an der RubisCO Aktivierung beteiligt sind. Mit diesem
Screening Verfahren ist es nun möglich RubisCOs von bisher unkultivierten Mikroorganismen zu detektieren und deren Funktionsweise zu analysieren.Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO; EC 4.1.1.39) catalyzes the key and primary carbon fixation reaction of the Calvin Benson cycle (CB cycle). This unique enzyme is present in all plants, cyanobacteria and most autotrophic bacteria (phototrophs and chemolitoautotrophs) and is involved in the assimilation of most of the inorganic carbon fixed by all primary producers on Earth (>99.5%). Most studies that have enhanced our understanding of RubisCO functioning have been conducted with plants or cultured bacteria. The functionality of environmental RubisCOs as well as the importance of gene products encoded on flanking DNA regions is however still enigmatic. Currently no sequence independent
approach is available, that enables seeking of RubisCOs directly from the environment by functionality alone. Therefore, the vast majority of functional RubisCOs and RubisCO associated genes from uncultured organisms (>99%) remains inaccessible. This study describes a novel, function-based approach suited to seek RubisCO active enzymes directly from metagenomic libraries. Within this study twelve environmental,
recombinant RubisCOs were identified through this screen and resembled genes form Thiomicrospira crunogena. The 35.2 kb comprising metagenomic fragments consist of a RubisCO gene cluster and flanking DNA regions. The relevance of potential RubisCO associated genes for expressing a fully functional RubisCO was further investigated for
one clone exemplarily, by making single genes inoperative due to transposon insertions. This approach uncovered one gene (orf06) whose gene product has never been associated with RubisCO activity before, but is directly or indirectly involved in positively regulating the transcription of cbbM and cbbL. Significantly changed RubisCO activities were furthermore found for clones with insertions in eleven other genes, whose gene products were assigned to functions of putative transcriptional regulators or those believed to be vital for RubisCO activation. This screen opens the door to detect up until now unexplored RubisCOs from the otherwise inaccessible
uncultured majority and enables us to better understand the functioning of prokaryotic RubisCOs
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