Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas

Biophysical Chemistry 110 (2004) 83–92

Deciphering the genome of Desulfovibrio gigas: the role of the hydrogenases

The work presented in this thesis describes the functional characterization of hydrogenases in the overall energy metabolism of the sulfate reducing bacterium Desulfovibrio gigas. With the complete annotation of the D. gigas genome, we were able to verify that only the two previously described hydrogenases are present in this organism, the periplasmic [NiFe] HynAB and the cytoplasmic membrane-bound [NiFe] Ech.(...)

Speziation mikrobiologisch alkylierter, leichtflüchtiger Selenverbindungen in Abhängigkeit der geochemischen Verfügbarkeit des Selens

Selen kann in verschiedenen Oxidationszuständen (+6, +4, ±0, -2) in unterschiedlichen Umweltkompartimenten auftreten. Verbundenen damit sind verschiedene Eigenschaften, wie z. B. die Wasserlöslichkeit, die in direktem Zusammenhang mit der Migrationsfähigkeit sowie der Bioverfügbarkeit steht. Im Rahmen der vorliegenden Arbeit wurden die Verfügbarkeit anorganischer Selenspezies und damit die Mobilisierbarkeit dieser in verschiedenen Laborexperimenten untersucht. Hierbei wurde an Goethit adsorbiertes Selenit sowohl mit einer Reinkultur des aktiv methylierenden Pilzes Alternaria alternata als auch mit einer angereicherten Umweltmischkultur inkubiert und die mikrobiologische Zugänglichkeit anhand der Bildung leichtflüchtiger, alkylierter Selenmetabolite wie z. B. Dimethylselenid und Dimethyldiselenid beobachtet. Zur Analyse dieser wurde eine cryotrapping-cryofocussing-GC-ICP-MS-Kopplung etabliert. Die Anteile der methylierten Selenverbindungen stiegen bei Verwendung von A. alternata mit der Inkubationszeit auf 10 % des gelösten Selens und 1 % des Gesamtselens an. Dieser Trend konnte während der Inkubation der Umweltmischkultur nicht beobachtet werden. Hier lagen die Anteile über den gesamten Untersuchungszeitraum bei ca. 0,5 % des gelösten bzw. 0,1 % des Gesamtselens, inklusive eines leichten Abwärtstrends, welcher wahrscheinlich durch die Nutzung der Alkylselenide als Kohlenstoffquelle hervorgerufen wurde. Weiterhin wurde das reduzierte Eisenselenidmineral Ferroselit eingesetzt, um dessen Stabilität gegenüber der Aktivität des sulfatreduzierenden Bakteriums Desulfovibrio gigas zu untersuchen. Mit zunehmender Inkubationszeit und damit verbundener, zunehmender Reduktion des im Nährmedium vorhandenen Sulfates konnte ein Anstieg leichtflüchtiger Organoselenverbindungen in der Gasphase der Kulturansätze festgestellt werden, die im unteren Nanogrammbereich lagen. Einhergehend damit wurde auch die Zunahme der Gehalte an gelöstem Selen und somit die biologisch bedingte Rücklösung aus der Mineral- in die Wasserphase beobachtet. Es konnte gezeigt werden, dass die Aktivität von Mikroorganismen einen deutlichen Einfluss auf die Stabilität von Oberflächenkomplexen des Selenits als auch von mineralischen Selenidspezies hat.

A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes.

The crystal structure of the xanthine oxidase-related molybdenum-iron protein aldehyde oxido-reductase from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas (Mop) was analyzed in its desulfo-, sulfo-, oxidized, reduced, and alcohol-bound forms at 1.8-A resolution. In the sulfo-form the molybdenum molybdopterin cytosine dinucleotide cofactor has a dithiolene-bound fac-[Mo, = O, = S, ---(OH2)] substructure. Bound inhibitory isopropanol in the inner compartment of the substrate binding tunnel is a model for the Michaelis complex of the reaction with aldehydes (H-C = O,-R). The reaction is proposed to proceed by transfer of the molybdenum-bound water molecule as OH- after proton transfer to Glu-869 to the carbonyl carbon of the substrate in concert with hydride transfer to the sulfido group to generate [MoIV, = O, -SH, ---(O-C = O, -R)). Dissociation of the carboxylic acid product may be facilitated by transient binding of Glu-869 to the molybdenum. The metal-bound water is replenished from a chain of internal water molecules. A second alcohol binding site in the spacious outer compartment may cause the strong substrate inhibition observed. This compartment is the putative binding site of large inhibitors of xanthine oxidase.

Microbial community of black band disease on infection, healthy and dead part of scleractinian Montipora sp. colony at Seribu islands, Indonesia

It is crucial to understand the microbial community associated with the host when attempting to discern the pathogen responsible for disease outbreaks in scleractinian corals. This study determines changes in the bacterial community associated with Montipora sp. in response to black band disease in Indonesian waters. Healthy, diseased, and dead Montipora sp. (n = 3 for each sample type per location) were collected from three different locations (Pari Island, Pramuka Island, and Peteloran Island). DGGE (Denaturing Gradient Gel Electrophoresis) was carried out to identify the bacterial community associated with each sample type and histological analysis was conducted to identify pathogens associated with specific tissues. Various Desulfovibrio species were found as novelty to be associated with infection samples, including Desulfovibrio desulfuricans, Desulfovibrio magneticus, and Desulfovibrio gigas, Bacillus benzoevorans, Bacillus farraginis in genus which previously associated with pathogenicity in corals. Various bacterial species associated with uninfected corals were lost in diseased and dead samples. Unlike healthy samples, coral tissues such as the epidermis, endodermis, zooxanthellae were not present on dead samples under histological observation. Liberated zooxanthellae and cyanobacteria were found in black band diseased Montipora sp. samples.

Behavior ecology of the Humboldt squid, Dosidicus gigas: insights from an animal-borne video and data logging system

Dosidicus gigas is a large pelagic cephalopod of the eastern Pacific that has recently undergone an unexpected, significant range expansion up the coast of North America. The impact that such a range expansion is expected to have on local fisheries and marine ecosystems has motivated a thorough study of this top predator, a squid whose lifestyle has been quite mysterious until recently. Unfortunately, Dosidicus spends daylight hours at depths prohibitive to making observations without significant artificial interference. Observations of this squid‟s natural behaviors have thus far been considerably limited by the bright illumination and loud noises of remotely-operated-vehicles, or else the presence of humans from boats or with SCUBA. However, recent technological innovations have allowed for observations to take place in the absence of humans, or significant human intrusion, through the use of animal-borne devices such as National Geographic‟s CRITTERCAM. Utilizing the advanced video recording and data logging technology of this device, this study seeks to characterize unknown components of Dosidicus gigas behavior at depth. Data from two successful CRITTERCAM deployments reveal an assortment of new observations concerning Dosidicus lifestyle. Tri-axial accelerometers enable a confident description of Dosidicus orientation during ascents, descents, and depth maintenance behavior - previously not possible with simple depth tags. Video documentation of intraspecific interactions between Dosidicus permits the identification of ten chromatic components, a previously undescribed basal chromatic behavior, and multiple distinct body postures. And finally, based on visualizations of spermatophore release by D. gigas and repetitive behavior patterns between squid pairs, this thesis proposes the existence of a new mating behavior in Dosidicus. This study intends to provide the first glimpse into the natural behavior of Dosidicus, establishing the groundwork for a comprehensive ethogram to be supported with data from future CRITTERCAM deployments. Cataloguing these behaviors will be useful in accounting for Dosidicus‟ current range expansion in the northeast Pacific, as well as to inform public interest in the impacts this expansion will have on local fisheries and marine ecosystems.

Tagging studies on the jumbo squid (Dosidicus gigas) in the Gulf of California, Mexico

Dosidicus gigas, the only species in the genus Dosidicus, is commonly known as the jumbo squid, jumbo flying squid (FAO, see Roper et al., 1984), or Humboldt squid. It is the largest ommastrephid squid and is endemic to the Eastern Pacific, ranging from northern California to southern Chile and to 140oW at the equator (Nesis, 1983; Nigmatullin, et al., 2001). During the last two decades it has become an extremely important fisheries resource in the Gulf of California (Ehrhardt et al., 1983; Morales-Bojórquez et al., 2001), around the Costa Rica Dome (Ichii et al., 2002) and off Peru (Taipe et al., 2001). It is also an active predator that undoubtedly has an important impact on local ecology in areas where it is abundant (Ehrhardt et al., 1983; Nesis, 1983; Nigmatullin et al., 2001; Markaida and Sosa-Nishizaki, 2003).

The Status of Queen Conch, Strombus gigas, Research in the Caribbean

Today there are approximately 230 published scientific papers on queen conch, Strombus gigas. Publication on this species began in the 1960's and increased rapidly during the 1980's and 1990's (Fig. 1). The increase in publication after 1980 was associated with three particular areas ofendeavor. First, many articles were published to document the rapid depletion of conch stocks throughout the Caribbean Sea. Second, substantial progress was made in understanding processes related to growth, mortality, and reproduction in queen conch. Third, because of the apparent and widespread decline in conch, several research laboratories, especially in Florida, Puerto Rico, Venezuela, and the Turks and Caicos Islands began experiments related to hatchery production of juvenile conch. The primary intent was to replenish wild stocks by releasing hatchery-reared animals. Today, hatchery production has been relatively well perfected, and the increase in numbers of scientific papers related specifically to culture has slowed. A thorough review of the history of conch mariculture was provided by Creswell (1994), and Davis (1994) summarized the details of larval culture technique.