Cyanobacteria may possess several enzymes that are directly involved in dihydrogen metabolism: nitrogenase(s) catalyzing the production of hydrogen concomitantly with the reduction of dinitrogen to ammonia, an uptake hydrogenase (encoded by hupSL) catalyzing the consumption of hydrogen produced by the nitrogenase, and a bidirectional hydrogenase (encoded by hoxFUYH) which has the capacity to both take up and produce hydrogen. This review summarizes our knowledge about cyanobacterial hydrogenases, focusing on recent progress since the first molecular information was published in 1995. It presents the molecular knowledge about cyanobacterial hupSL and hoxFUYH, their corresponding gene products, and their accessory genes before finishing with an applied aspect—the use of cyanobacteria in a biological, renewable production of the future energy carrier molecular hydrogen. In addition to scientific publications, information from three cyanobacterial genomes, the unicellular Synechocystis strain PCC 6803 and the filamentous heterocystous Anabaena strain PCC 7120 and Nostoc punctiforme (PCC 73102/ATCC 29133) is included

Nanopore based DNA-sequencing delivers long reads, thereby simplifying the decipherment of bacterial communities. Since its commercial appearance, this technology has been assigned several attributes, such as its error proneness, comparatively low cost, ease-of-use, and, most notably, aforementioned long reads. The technology as a whole is under continued development. As such, benchmarks are required to conceive, test and improve analysis protocols, including those related to the understanding of the composition of microbial communities. Here we present a dataset composed of twelve different prokaryotic species split into four samples differing by nucleic acid quantification technique to assess the specificity and sensitivity of the MinION nanopore sequencer in a blind study design. Taxonomic classification was performed by standard taxonomic sequence classification tools, namely Kraken, Kraken2 and Centrifuge directly on reads. This allowed taxonomic assignments of up to 99.27% on genus level and 92.78% on species level, enabling true-positive classification of strains down to 25,000 genomes per sample. Full genomic coverage is achieved for strains abundant as low as 250,000 genomes per sample under our experimental settings. In summary, we present an evaluation of nanopore sequence processing analysis with respect to microbial community composition. It provides an open protocol and the data may serve as basis for the development and benchmarking of future data processing pipelines.

The green alga Scenedesmus obliquus is capable of both uptake and production of H(2) after anaerobic adaptation (photoreduction of CO(2) or photohydrogen production). The essential enzyme for H(2)-metabolism is a NiFe-hydrogenase with a [2Fe-2S]-ferredoxin as its natural redox partner. Western blot analysis showed that the hydrogenase is constitutively expressed. The K(m) values were 79.5 microM and 12.5 microM, determined with ferredoxin and H(2), respectively, as electron donor for the hydrogenase. In vitro, NADP(+) was reduced by H(2) in the presence of the hydrogenase, the ferredoxin and a ferredoxin-NADP reductase. From these results and considerations on the stoichiometry we propose that this light-independent electron transfer is part of the photoreduction of CO(2) in vivo. For ATP synthesis, necessary for the photoreduction of CO(2), light-dependent cyclic electron transfer around Photosystem (PS) I accompanies this 'dark reaction'. PS II fluorescence data suggest that (a) in S. obliquus H(2)-reduction might function as the anaerobic counterpart of the O(2)-dependent Mehler reaction, and (b) the presence of either a ferredoxin quinone-reductase or NAD(P)-dehydrogenase (complex I) in S. obliquus chloroplasts.

Bumble bees are important crop pollinators and provide important pollination services to their respective ecosystems. Their pollen diet and thus food preferences can be characterized through nucleic acid sequence analysis. We present ITS2 amplicon sequence data from pollen collected by bumble bees. The pollen was collected from six different bumble bee colonies that were placed in independent agricultural landscapes. We compared next-generation (Illumina), i.e., short-read, and thirdgeneration (Nanopore), i.e., MinION, sequencing techniques. MinION data were preprocessed using traditional and Nanopore specific tools for comparative analysis and were evaluated in comparison to short-read sequence data with conventional processing. Based on the results, the dietary diary of bumble bee in the studied landscapes can be identified. It is known that short reads generated by next-generation sequencers have the advantage of higher quality scores while Nanopore yields longer read lengths. We show that assignments to taxonomic units yield comparable results when querying against an ITS2-specific sequence database. Thus, lower sequence quality is compensated by longer read lengths. However, the Nanopore technology is improving in terms of data quality, much cheaper, and suitable for portable applications. With respect to the studied agricultural landscapes we found that bumble bees require higher plant diversity than only crops to fulfill their foraging requirements.

Fe-hydrogenase-specific degenerate primers were used in polymerase chain reactions with single-stranded Scenedesmus obliquus cDNA as template. A resulting 435-bp fragment was used to screen a cDNA library from S. obliquus. A 1.6-kb cDNA clone, containing the 3'-end of an open reading frame, was obtained. Its deduced amino acid sequence contains the conserved H-cluster motives unique for Fe-hydrogenases. Any other FeS-clusters seem to be absent. Phylogenetically, the enzyme is closely related to the Trichomonas vaginalis Fe-hydrogenase. Northern blot analysis shows that the Fe-hydrogenase is constitutively expressed in S. obliquus. Southern blot analysis of plastidic, mitochondrial, and nuclear DNA reveals that the enzyme is a single-copy gene encoded in the nucleus. Effects of transcriptional and translational inhibitors on H2-metabolism reveal the involvement of a chloroplast-encoded protein.