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

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants

Background: In biogas plants, complex microbial communities produce methane and carbon dioxide by anaerobic digestion of biomass. For the characterization of the microbial functional networks, samples of 11 reactors were analyzed using a high-resolution metaproteomics pipeline. Results: Examined methanogenesis archaeal communities were either mixotrophic or strictly hydrogenotrophic in syntrophy with bacterial acetate oxidizers. Mapping of identified metaproteins with process steps described by the Anaerobic Digestion Model 1 confirmed its main assumptions and also proposed some extensions such as syntrophic acetate oxidation or fermentation of alcohols. Results indicate that the microbial communities were shaped by syntrophy as well as competition and phage-host interactions causing cell lysis. For the families Bacillaceae, Enterobacteriaceae, and Clostridiaceae, the number of phages exceeded up to 20-fold the number of host cells. Conclusion: Phage-induced cell lysis might slow down the conversion of substrates to biogas, though, it could support the growth of auxotrophic microbes by cycling of nutrients. © 2019 The Author(s)

A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.

peer reviewed[en] BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts. RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin. CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.Explor‑ ing the higher termite lignocellulolytic system to optimise the conversion of biomass into energy and useful platform molecule

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

Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate

published_or_final_versio

Isolation and characterization of a new [FeFe]-hydrogenase from Clostridium perfringens

© 2015 International Union of Biochemistry and Molecular Biology, Inc. This paper reports the first characterization of an [FeFe]-hydrogenase from a Clostridium perfringens strain previously isolated in our laboratory from a pilot-scale bio-hydrogen plant that efficiently produces H2 from waste biomasses. On the basis of sequence analysis, the enzyme is a monomer formed by four domains hosting various iron–sulfur centres involved in electron transfer and the catalytic center H-cluster. After recombinant expression in Escherichia coli, the purified protein catalyzes H2 evolution at high rate of 1645±16s−1. The optimal conditions for catalysis are in the pH range 6.5–8.0 and at the temperature of 50°C. EPR spectroscopy showed that the H-cluster of the oxidized enzyme displays a spectrum coherent with the Hox state, whereas the CO-inhibited enzyme has a spectrum coherent with the Hox-CO state. FTIR spectroscopy showed that the purified enzyme is composed of a mixture of redox states, with a prevalence of the Hox; upon reduction with H2, vibrational modes assigned to the Hred state were more abundant, whereas binding of exogenous CO resulted in a spectrum assigned to the Hox-CO state. The spectroscopic features observed are similar to those of the [FeFe]-hydrogenases class, but relevant differences were observed given the different protein environment hosting the H-cluster

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

Unveiling microbial structures during raw microalgae digestion and co-digestion with primary sludge to produce biogas using semi-continuous AnMBR systems

[EN] Methane production from microalgae can be enhanced through anaerobic co-digestion with carbon-rich substrates and thus mitigate the inhibition risk associated with its low C:N ratio. Acclimated microbial communities for microalgae disruption can be used as a source of natural enzymes in bioenergy production. However, co-substrates with a certain microbial diversity such as primary sludge might shift the microbial structure. Substrates were generated in a Water Resource Recovery Facility (WRRF) and combined as follows: Scenedesmus or Chlorella digestion and microalgae co-digestion with primary sludge. The study was performed using two lab-scale Anaerobic Membrane Bioreactors (AnMBR). During three years, different feedstocks scenarios for methane production were evaluated with a special focus on the microbial diversity of the AnMBR. 57% of the population was shared between the different feedstock scenarios, revealing the importance of Anaerolineaceae members besides Smithella and Methanosaeta genera. The addition of primary sludge enhanced the microbial diversity of the system during both Chlorella and Scenedesmus co-digestion and promoted different microbial structures. Aceticlastic methanogen Methanosaeta was dominant in all the feedstock scenarios. A more remarkable role of syntrophic fatty acid degraders (Smithella, Syntrophobacteraceae) was observed during co-digestion when only microalgae were digested. However, no significant changes were observed in the microbial composition during anaerobic microalgae digestion when feeding only Chlorella or Scenedesmus. This is the first work revealing the composition of complex communities for semi-continuous bioenergy production from WRRF streams. The stability and maintenance of a microbial core over-time in semi-continuous AnMBRs is here shown supporting their future application in full-scale systems for raw microalgae digestion or codigestion.The Ministry of Economy and Competitiveness (MINECO) and the European Regional Development Fund (ERDF) are gratefully acknowledged for their support to this research work through CTM2011-28595-C02-02 and CTM2014-54980-C2-1-R projects. The authors are thankful to Ph.D. Silvia Greses and Ph.D. candidate Rebecca Serna-Garcia (Universitat de Valencia, Spain) for allowing the collection of digestate samples from their bioreactors and providing a brief data characterization of their performance. As well, authors thank the support of Maria Paches (IIAMA, Valencia, Spain) during phytoplankton monitoring in the photobioreactor plant. Finally, the sequencing service from FISABIO (Valencia, Spain) is also gratefully acknowledged for their technical support during the design stage of this work.Zamorano-López, N.; Borrás, L.; Seco, A.; Aguado García, D. (2020). Unveiling microbial structures during raw microalgae digestion and co-digestion with primary sludge to produce biogas using semi-continuous AnMBR systems. The Science of The Total Environment. 699:1-12. https://doi.org/10.1016/j.scitotenv.2019.134365S112699APHA, APHA/AWWA/WEF, 2012. In: Standard Methods for the Examination of Water and Wastewater. Stand. Methods, pp. 541 doi.org/ISBN 9780875532356.Astals, S., Musenze, R. S., Bai, X., Tannock, S., Tait, S., Pratt, S., & Jensen, P. D. (2015). Anaerobic co-digestion of pig manure and algae: Impact of intracellular algal products recovery on co-digestion performance. Bioresource Technology, 181, 97-104. doi:10.1016/j.biortech.2015.01.039Baudelet, P.-H., Ricochon, G., Linder, M., & Muniglia, L. (2017). 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Optimized Expression and Purification for High-Activity Preparations of Algal [FeFe]-Hydrogenase

Background: Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crystallographic studies. Principal Findings: We describe the construction, overexpression and high-yield purification of a fusion protein consisting of the algal [2Fe2S]-ferredoxin PetF (Fd) and [FeFe]-hydrogenase HydA1. The maturation of Fd-HydA1 was optimized through improvements in culture conditions and media components used for expression. We also demonstrated that fusion of Fd to the N-terminus of HydA1, in comparison to the C-terminus, led to increased expression levels that were 4-fold higher. Together, these improvements led to enhanced HydA1 activity and improved yield after purification. The strong binding-affinity of Fd for DEAE allowed for two-step purification by ion exchange and StrepTactin affinity chromatography. In addition, the incorporation of a TEV protease site in the Fd-HydA1 linker allowed for the proteolytic removal of Fd after DEAE step, and purification of HydA1 alone by StrepTactin. In combination, this process resulted in HydA1 purification yields of 5 mg L−1 of culture from E. coli with specific activities of 1000 U (U = 1 µmol hydrogen evolved mg−1 min−1). Significance: The [FeFe]-hydrogenases are highly efficient enzymes and their catalytic sites provide model structures for synthetic efforts to develop robust hydrogen activation catalysts. In order to characterize their structure-function properties in greater detail, and to use hydrogenases for biotechnological applications, reliable methods for rapid, high-yield expression and purification are required.United States. Dept. of Energy. (contract DE-AC36-08-GO28308