Syntrophic propionate-oxidizing bacteria in methanogenic systems

This review summarizes discoveries in syntrophic propionate degradation research and reveals intriguing metabolic capabilities, mechanisms of cooperation and environmentally driven kinetics by taxonomically distinct microorganisms that are important for biotechnological applications and biogenic methane emissions.The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes

The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals

Background: Aquaporins are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. These proteins are vital for maintaining water homeostasis in living organisms. In mammals, thirteen aquaporins (AQP0-12) have been characterized, but in lower vertebrates, such as fish, the diversity, structure and substrate specificity of these membrane channel proteins are largely unknown. Results: The screening and isolation of transcripts from the zebrafish (Danio rerio) genome revealed eighteen sequences structurally related to the four subfamilies of tetrapod aquaporins, i.e., aquaporins (AQP0, -1 and -4), water and glycerol transporters or aquaglyceroporins (Glps; AQP3 and AQP7-10), a water and urea transporter (AQP8), and two unorthodox aquaporins (AQP11 and -12). Phylogenetic analyses of nucleotide and deduced amino acid sequences demonstrated dual paralogy between teleost and human aquaporins. Three of the duplicated zebrafish isoforms have unlinked loci, two have linked loci, while DrAqp8 was found in triplicate across two chromosomes. Genomic sequencing, structural analysis, and maximum likelihood reconstruction, further revealed the presence of a putative pseudogene that displays hybrid exons similar to tetrapod AQP5 and -1. Ectopic expression of the cloned transcripts in Xenopus laevis oocytes demonstrated that zebrafish aquaporins and Glps transport water or water, glycerol and urea, respectively, whereas DrAqp11b and -12 were not functional in oocytes. Contrary to humans and some rodents, intrachromosomal duplicates of zebrafish AQP8 were water and urea permeable, while the genomic duplicate only transported water. All aquaporin transcripts were expressed in adult tissues and found to have divergent expression patterns. In some tissues, however, redundant expression of transcripts encoding two duplicated paralogs seems to occur. Conclusion: The zebrafish genome encodes the largest repertoire of functional vertebrate aquaporins with dual paralogy to human isoforms. Our data reveal an early and specific diversification of these integral membrane proteins at the root of the crown-clade of Teleostei. Despite the increase in gene copy number, zebrafish aquaporins mostly retain the substrate specificity characteristic of the tetrapod counterparts. Based upon the integration of phylogenetic, genomic and functional data we propose a new classification for the piscine aquaporin superfamily

Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009

[en] Background: Molecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels infuture transportation and energy production. However, current industrial hydrogen production processes, such assteam reforming of methane, contribute significantly to the greenhouse effect. Therefore alternative methods, inparticular the use of fermentative microorganisms, have attracted scientific interest in recent years. However thelow overall yield obtained is a major challenge in biological H2 production. Thus, a thorough and detailedunderstanding of the relationships between genome content, gene expression patterns, pathway utilisation andmetabolite synthesis is required to optimise the yield of biohydrogen production pathways.Results: In this study transcriptomic and proteomic analyses of the hydrogen-producing bacterium Clostridiumbutyricum CWBI 1009 were carried out to provide a biomolecular overview of the changes that occur when themetabolism shifts to H2 production. The growth, H2-production, and glucose-fermentation profiles were monitoredin 20 L batch bioreactors under unregulated-pH and fixed-pH conditions (pH 7.3 and 5.2). Conspicuous differenceswere observed in the bioreactor performances and cellular metabolisms for all the tested metabolites, and theywere pH dependent. During unregulated-pH glucose fermentation increased H2 production was associated withconcurrent strong up-regulation of the nitrogenase coding genes. However, no such concurrent up-regulation ofthe [FeFe] hydrogenase genes was observed. During the fixed pH 5.2 fermentation, by contrast, the expressionlevels for the [FeFe] hydrogenase coding genes were higher than during the unregulated-pH fermentation, whilethe nitrogenase transcripts were less abundant. The overall results suggest, for the first time, that environmentalfactors may determine whether H2 production in C. butyricum CWBI 1009 is mediated by the hydrogenases and/orthe nitrogenase.Conclusions: This work, contributing to the field of dark fermentative hydrogen production, provides amultidisciplinary approach for the investigation of the processes involved in the molecular H2 metabolism ofclostridia. In addition, it lays the groundwork for further optimisation of biohydrogen production pathways basedon genetic engineering techniques.info:eu-repo/semantics/publishe

SISTEM PENDUKUNG KEPUTUSAN POLA OLAHRAGA BERDASARKAN HASIL YANG INGIN DICAPAI MENGGUNAKAN FUZZY DATABASE MODEL TAHANI

Pada saat ini, perkembangan di dunia kesehatan telah berkembang secara cepat sehingga mendorong para ahli untuk merancang sebuah teknologi yang dapat mengambil keputusan didalam bidang kesehatan. Kesehatan merupakan hal sangat mahal dan sangat penting bagi keberlangsungan hidup manusia. Untuk mendapatkan tubuh yang sehat tentunya di butuhkan olahraga yang teratur. Olahraga dilakukan juga harus dengan porsi yang dibutuhkan oleh tubuh. Ketidaktahuan akan porsi olahraga yang dibutuhkan oleh tubuh manusia ini yang menjadi masalah bagi kebanyakan orang. Penelitian ini menggunakan metode studi literature dalam pengumpulan data serta fuzzy database model tahani. Pengembangan sistemnya menggunakan metode waterfall. Pemodelan analisis dan desain menggunakan bahasa pemograman PHP dan database server MySQL. Metode pengujian menggunakan pengujian white box.  Hasil penelitian ini adalah sebuah sistem pendukung keputusan pola olahraga berbasis website yang dapat memudahkan pengguna dalam menentukan pola olahraga yang cocok dilakukan sesuai data kriteria yaitu umur, berat badan dan tinggi badan

ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

BACKGROUND: Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called "microbial dark matter" (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus. Furthermore, these software tools typically lack a provision for the visualization of data and bin characteristics. RESULTS: We present ICoVeR, the Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins. More specifically, ICoVeR allows curation of bin assignments based on multiple binning algorithms. Its visualization window is composed of two connected and interactive main views, including a parallel coordinates view and a dimensionality reduction plot. To demonstrate ICoVeR's utility, we used it to refine disparate genome bins automatically generated using MetaBAT, CONCOCT and MyCC for an anaerobic digestion metagenomic (AD microbiome) dataset. Out of 31 refined genome bins, 23 were characterized with higher completeness and lower contamination in comparison to their respective, automatically generated, genome bins. Additionally, to benchmark ICoVeR against a previously validated dataset, we used Sharon's dataset representing an infant gut metagenome. CONCLUSIONS: ICoVeR is an open source software package that allows curation of disparate genome bins generated with automatic binning algorithms. It is freely available under the GPLv3 license at https://git.list.lu/eScience/ICoVeR . The data management and analytical functions of ICoVeR are implemented in R, therefore the software can be easily installed on any system for which R is available. Installation and usage guide together with the example files ready to be visualized are also provided via the project wiki. ICoVeR running instance preloaded with AD microbiome and Sharon's datasets can be accessed via the website

Application of molecular tools to study the hydrogen production by the bacteria of the genus Clostridium

L’hydrogène moléculaire a un potential énorme comme futur vecteur énergétique car sa combustion n’est pas polluante. Cependant, les processus industriels actuels de production contribuent substantiellement à l’effet de serre. Au contraire, une production d’H2 qui est neutre en CO2 peut être obtenue par la fermentation anaérobique obscure. Les bactéries du genre Clostridium peuvent fermenter les sucres en H2 et CO2 avec production d’ acide acétique et butyrique qui servent d’accepteurs principaux d’électrons. Cependant, en fonction de la souche/co-culture utilisée et des conditions de culture, des composés plus réduits peuvent être obtenus, par ex. l’éthanol, le lactate, ce qui réduit substantiellement le rendement final en H2. De plus, les différentes voies métaboliques et les circuits de régulation conduisant à la production d’H2 dans les clostridies ne sont pas bien connus. Dans cette étude, nous avons étudié deux sujets principaux. D’une part, nous avons étudié différentes co-cultures de Clostridium spp. dans des bioréacteurs produisant de l’H2. En suivant les co-cultures de C. butyricum et C. pasteurianum par FISH (Fluorescence in situ hybridisation) et qPCR (quantitative real-time PCR), nous avons montré que les deux espèces co-existent de manière stable durant la fermentation de différents sucres dans deux bioréacteurs. D’autre part, en utilisant Clostridium butyricum CWBI1009 comme modèle, nous avons étudié le métabolisme complexe de l’H2 chez les clostridies. La découverte de gènes nouveaux codant pour des hydrogènases [FeFe] dans les génomes séquencés a changé notre vue de la façon dont ces microbes produisent l’ H2. En effet, en utilisant différents outils moléculaires (2D-DIGE, RT-qPCR et RNA-seq), nous avons montré que dans différents conditions de milieu, différentes hydrogénases contribuent à la production d’H2. De plus, sous atmosphère d’N2 pendant la fermentation du glucose dans des conditions de pH non régulées, nous observons que la nitrogénase contribue à la production globale d’H2. De manière surprenante, alors que les clostridies semblent bien équipées pour produire de l’H2, elles n’ont probablement développé cette capacité que pour s’adapter rapidement aux variations de conditions, cad la diminution du pH. Donc, pour maintenir un pH intracellulaire constant, elles rejettent les protons (sans doute sous forme de H2) dans le milieu. Ainsi, elles se débarrassent de l’excès d’équivalents réducteurs produits pendant la fermentation du glucose. En résumé, nos résultats contribuent à une meilleure connaissance du métabolisme complexe de l’H2 chez les clostridies. Cependant, un défi pour le futur consiste à caractériser les enzymes responsables de ce métabolisme et, par bioengineering métabolique, de développer des systèmes microbiens optimaux pour la conversion de la biomasse en H2.Fabrice Franc

The diversity of clostridial hydrogenases revealed by genome sequencing projects

Molecular hydrogen is a key intermediate in metabolomic interactions of a wide range of microorganisms. Hydrogen is also regarded as a key component in future energy systems as it is a sustainable, clean, and transportable energy carrier. Some microorganisms can produce hydrogen during a reversible reduction of protons to dihydrogen, a reaction which is catalyzed by the enzyme hydrogenases. On the basis of their bimetallocenter composition, hydrogenases are divided into three main groups, phylogenetically not related: [NiFe] hydrogenases, [Fe] only hydrogenases and FeS cluster free hydrogenases. The latter were described in methanogenic Archaea only. [NiFe] hydrogenases, composed of at least two subunits are well characterized and widely distributed between Archaea and Bacteria. However, only a few representatives of Clostridium sp. possess this type of enzyme. On the other hand, much less is known about the [Fe] only hydrogenases, that are usually monomeric enzymes and restricted to Bacteria and a few eukaryotic species. Genome sequencing projects gave a completely new insight into the diversity of forms of putative [Fe] only hydrogenases within the genus Clostridium. With the use of bioinformatic tools, we have described the unusual modularity of forms of these enzymes, from monomeric to tetrameric with a different number of accessory domains reacting with diverse redox partners. This fact seems to support the central role of hydrogenases in cell metabolism and quick adaptation of the host to changing environmental conditions. Moreover, the presence of multiple putative operons encoding for multisubunit [FeFe] hydrogenases is highlighting the fact that hydrogen metabolism is very complex in the Clostridium genus

The diversity of clostridial hydrogenases revealed by genome sequencing projects

Molecular hydrogen is a key intermediate in metabolomic interactions of a wide range of microorganisms. Hydrogen is also regarded as a key component in future energy systems as it is a sustainable, clean, and transportable energy carrier. Some microorganisms can produce hydrogen during a reversible reduction of protons to dihydrogen, a reaction which is catalyzed by the enzyme hydrogenases. On the basis of their bimetallocenter composition, hydrogenases are divided into three main groups, phylogenetically not related: [NiFe] hydrogenases, [Fe] only hydrogenases and FeS cluster free hydrogenases. The latter were described in methanogenic Archaea only. [NiFe] hydrogenases, composed of at least two subunits are well characterized and widely distributed between Archaea and Bacteria. However, only a few representatives of Clostridium sp. possess this type of enzyme. On the other hand, much less is known about the [Fe] only hydrogenases, that are usually monomeric enzymes and restricted to Bacteria and a few eukaryotic species. Genome sequencing projects gave a completely new insight into the diversity of forms of putative [Fe] only hydrogenases within the genus Clostridium. With the use of bioinformatic tools, we have described the unusual modularity of forms of these enzymes, from monomeric to tetrameric with a different number of accessory domains reacting with diverse redox partners. This fact seems to support the central role of hydrogenases in cell metabolism and quick adaptation of the host to changing environmental conditions. Moreover, the presence of multiple putative operons encoding for multisubunit [FeFe] hydrogenases is highlighting the fact that hydrogen metabolism is very complex in the Clostridium genus