Formate formation and formate conversion in biological fuels production

Multi-omics analysis unravels effects of salt and oil on substance transformation, microbial community, and transcriptional activity in food waste anaerobic digestion

In this study, through quantitative detection of key substances and enzyme activities, an integrated analysis of 16S rRNA sequencing and metatranscriptomics revealed the mechanisms by which salt and oil influence the biotransformation process during anaerobic digestion (AD). The results demonstrated that a salt concentration of 6 g/L promoted lipid metabolism and hydrogenotrophic methanogenesis, while inhibiting the acetoclastic pathway. An oil concentration of 5 g/L facilitated the expression of key enzyme-encoding genes involved in β-oxidation of long-chain fatty acids, transcription, and acetoclastic methanogenesis. It also promoted the enrichment of syntrophic propionate/butyrate oxidation bacteria (Syntrophomonas and DMER64). Salt/oil co-addition enhanced the expression of genes related to glucose metabolism, amino acid metabolism, organic acid synthesis, and quorum sensing. Furthermore, salt/oil co-addition inhibited the secretion of key enzymes related to methanogens by impeding the transcription process. Collectively, these findings provide systematic insights into how salt and oil affect the biochemical metabolic mechanisms of AD.

Review: Diving into the cow hologenome to reduce methane emissions and increase sustainability

Interest on methane emissions from livestock has increased in later years as it is an anthropogenic greenhouse gas with an important warming potential. The rumen microbiota has a large influence on the production of enteric methane. Animals harbour a second genome consisting of microbes, collectively referred to as the "microbiome". The rumen microbial community plays an important role in feed digestion, feed efficiency, methane emission and health status. This review recaps the current knowledge on the genetic control that the cow exerts on the rumen microbiota composition. Heritability estimates for the rumen microbiota composition range between 0.05 and 0.40 in the literature, depending on the taxonomical group or microbial gene function. Variables depicting microbial diversity or aggregating microbial information are also heritable within the same range. This study includes a genome-wide association analysis on the microbiota composition, considering the relative abundance of some microbial taxa previously associated to enteric methane in dairy cattle (Archaea, Dialister, Entodinium, Eukaryota, Lentisphaerae, Methanobrevibacter, Neocallimastix, Prevotella and Stentor). Host genomic regions associated with the relative abundance of these microbial taxa were identified after Benjamini-Hoschberg correction (Padj < 0.05). An in-silico functional analysis using FUMA and DAVID online tools revealed that these gene sets were enriched in tissues like brain cortex, brain amigdala, pituitary, salivary glands and other parts of the digestive system, and are related to appetite, satiety and digestion. These results allow us to have greater knowledge about the composition and function of the rumen microbiome in cattle. The state-of-the art strategies to include methane traits in the selection indices in dairy cattle populations is reviewed. Several strategies to include methane traits in the selection indices have been studied worldwide, using bioeconomical models or economic functions under theoretical frameworks. However, their incorporation in the breeding programmes is still scarce. Some potential strategies to include methane traits in the selection indices of dairy cattle population are presented. Future selection indices will need to increase the weight of traits related to methane emissions and sustainability. This review will serve as a compendium of the current state of the art in genetic strategies to reduce methane emissions in dairy cattle.

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.

Effects of initial volatile fatty acid concentrations on process characteristics, microbial communities, and metabolic pathways on solid-state anaerobic digestion

Solid-state anaerobic digestion (SSAD) is vulnerable to excess volatile fatty acids (VFA), mainly acetate and propionate. The co-effects of VFAs and microbial dynamics under VFA accumulation were investigated in SSAD of pig manure and corn straw. Adding 2 and 4 mg/g acetate or propionate caused initial increases in total VFAs, followed by decreases after day 6, resulting in 'mild' VFA accumulation, while adding 6 mg/g caused similarly increased VFAs, but with no subsequent decrease, causing 'severe' VFA accumulation and poor methanation performance. Mild propionate accumulation promoted acetate consumption, whereas acetate accumulation inhibited propionate degradation by affecting crucial redox reactions. Under severe VFA accumulation, hydrolysis and acidification mainly conducted by acid-tolerant Clostridium sp. exacerbated VFA inhibition, causing a competition between Methanosarcina and Methanosaeta, and impairments of acetoclastic and hydrogenotrophic methanogenesis and interspecies formate transfer. This study provides new insights into mechanisms of VFA accumulation in SSAD, and its effects on methanogenesis.

Application of 1H HR-MAS NMR-Based Metabolite Fingerprinting of Marine Microalgae

Natural products from the marine environment as well as microalgae, have been known for the complexity of the metabolites they produce due to their adaptability to different environmental conditions, which has been an inexhaustible source of several bioactive properties, such as antioxidant, anti-tumor, and antimicrobial. This study aims to characterize the main metabolites of three species of microalgae (Nannochloropsis oceanica, Chaetoceros muelleri, and Conticribra weissflogii), which have important applications in the biofuel and nutrition industries, by ¹H High-resolution magic angle spinning nuclear magnetic resonance (¹H HR-MAS NMR), a method which is non-destructive, is highly reproducible, and requires minimal sample preparation. Even though the three species were found in the same ecosystem and a superior production of lipid compounds was observed, important differences were identified in relation to the production of specialized metabolites. These distinct properties favor the use of these compounds as leaders in the development of new bioactive compounds, especially against environmental, human, and animal pathogens (One Health), and demonstrate their potential in the development of alternatives for aquaculture.

pH and hydraulic retention time regulation for anaerobic fermentation: Focus on volatile fatty acids production/distribution, microbial community succession and interactive correlation

Enriching suitable fermentative products by optimizing operation conditions could effectively improve the efficiency of anaerobic digestion. In the present study, pH (5.0-6.0) and hydraulic retention time (HRT) (2 h-12 h) were regulated for volatile fatty acids (VFAs) production during glucose fermentation in acidogenic continuous stirred tank reactor (CSTR). Results showed that acetate and butyrate dominated during pH regulation. HRT reduction favored butyrate production and formate retainment. Maximum total VFAs production with highest acetate content was achieved at pH of 6.0 and HRT of 6 h. Microbial analysis revealed that Clostridium_sensu_stricto_1 was predominant butyrate producer during pH regulation, and Bacteroides was main contributor when HRT shorter than 6 h. In addition to acetyl-CoA pathway, acetate could also be produced via homoacetogenesis by Parabacteroides, UCG-004 and norank_f__Acidaminococcaceae. These results would give guidance for enhancing targeted VFAs products by optimizing operational parameters or bio-augmentation with specific bacteria.

Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle

Background

Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions.

Results

The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R² < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (P_adj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found to be differentially abundant between low- and high-emission animals and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals.

Conclusions

Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the relative abundance of Bacteria, Archaea, and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH₄ emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.

Inhibition of sulfate-reducing bacteria with formate

Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8 or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Concerning D. multivorans, increasing formate concentrations delayed the onsets of growth and sulfate reduction, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.

Operational and biochemical aspects of co-digestion (co-AD) from sugarcane vinasse, filter cake, and deacetylation liquor

This work performed co-AD from the vinasse and filter cake (from 1G ethanol production) and deacetylation liquor (from the pretreatment of sugarcane straw for 2G ethanol production) in a semi-Continuous Stirred Tank Reactor (s-CSTR) aiming to provide optimum operational parameters for continuous CH₄ production. Using filter cake as co-substrate may allow the reactor to operate throughout the year, as it is available in the sugarcane off-season, unlike vinasse. A comparison was made from the microbial community of the seed sludge and the reactor sludge when CH₄ production stabilized. Lactate, butyrate, and propionate fermentation routes were denoted at the start-up of the s-CSTR, characterizing the acidogenic phase: the oxidation-reduction potential (ORP) values ranged from -800 to -100 mV. Once the methanogenesis was initiated, alkalizing addition was no longer needed as its demand by the microorganisms was supplied by the alkali characteristics of the deacetylation liquor. The gradual increase of the applied organic load rates (OLR) allowed stabilization of the methanogenesis from 3.20 g_VS L^-1 day^-1: the highest CH₄ yield (230 mL_NCH₄ g^-1_VS) and average organic matter removal efficiency (83% ± 13) was achieved at ORL of 4.16 g_VS L^-1 day^-1. The microbial community changed along with the reactor operation, presenting different metabolic routes mainly due to the used lignocellulosic substrates. Bacteria from the syntrophic acetate oxidation (SAO) process coupled to hydrogenotrophic methanogenesis were predominant (~ 90% Methanoculleus) during the CH₄ production stability. The overall results are useful as preliminary drivers in terms of visualizing the co-AD process in a sugarcane biorefinery integrated to scale. KEY POINTS: • Integration of 1G2G sugarcane ethanol biorefinery from co-digestion of its residues. • Biogas production from vinasse, filter cake, and deacetylation liquor in a semi-CSTR. • Lignocellulosic substrates affected the biochemical routes and microbial community. • Biomol confirmed the establishment of the thermophilic community from mesophilic sludge.

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

Enzymes for Efficient CO2 Conversion

The accumulation of carbon dioxide in the atmosphere as a result of human activities has caused a number of adverse circumstances in the world. For this reason, the proposed solutions lie within the aim of reducing carbon dioxide emissions have been quite valuable. However, as the human activity continues to increase on this planet, the possibility of reducing carbon dioxide emissions decreases with the use of conventional methods. The emergence of compounds than can be used in different fields by converting the released carbon dioxide into different chemicals will construct a fundamental solution to the problem. Although electro-catalysis or photolithography methods have emerged for this purpose, they have not been able to achieve successful results. Alternatively, another proposed solution are enzyme based systems. Among the enzyme-based systems, pyruvate decarboxylase, carbonic anhydrase and dehydrogenases have been the most studied enzymes. Pyruvate dehydrogenase and carbonic anhydrase have either been an expensive method or were incapable of producing the desired result due to the reaction cascade they catalyze. However, the studies reporting the production of industrial chemicals from carbon dioxide using dehydrogenases and in particular, the formate dehydrogenase enzyme, have been remarkable. Moreover, reported studies have shown the existence of more active and stable enzymes, especially the dehydrogenase family that can be identified from the biome. In addition to this, their redesign through protein engineering can have an immense contribution to the increased use of enzyme-based methods in CO₂ reduction, resulting in an enormous expansion of the industrial capacity.

Deeper insights into effect of activated carbon and nano-zero-valent iron addition on acidogenesis and whole anaerobic digestion

Conductive materials presented promising advantages for enhancing anaerobic digestion (AD) performance. This study evaluated the effects of activated carbon (AC) and nano-zero-valent iron (nZVI) on the acidogenesis and whole AD to explore their potential mechanisms. AC increased the content of lactic and propionic acids in acidogenesis. nZVI increased the production of formic acid, acetic acid and H₂ in acidogenesis, thus significantly promoted the methane yield in the whole AD. Mechanism exploration proved that AC enriched Trichococcus, and norank_f__Bacteroidetes_vadinHA17, and then improved the activity of enzymes involved in the production of lactic and propionic acids. nZVI buffered the pH to increase the activity of pyruvate formate-lyase (PFL) in formic acid production. Furthermore, nZVI enriched the Methanobacterium which use H₂ and formic acid as substrate. The research paves pathway for the efficient enhancement of conductive materials added novel AD process.

Novel strategy for relieving acid accumulation by enriching syntrophic associations of syntrophic fatty acid-oxidation bacteria and H2/formate-scavenging methanogens in anaerobic digestion

Aiming at relieving acid accumulation in anaerobic digestion (AD), syntrophic associations of syntrophic fatty acid-oxidation bacteria and H₂/formate-scavenging methanogens were enriched by feeding propionate, butyrate and formate in an up-flow anaerobic sludge blanket (UASB) reactor. Results showed that methane yield increased by 50% with increasing formate concentration (0-2000 mg COD/L). In addition, the abundance and quantity of SFOB (Syntrophobacter, Smithella and Syntrophomonas) and H₂/formate-scavenging methanogens (Methanobacteriales and Methanomicrobiales) were increased after microbial acclimation. The enriched syntrophic associations showed higher propionate and butyrate removal efficiencies of 98.48 ± 1.14% and 99.71 ± 0.71%, respectively. Furthermore, encoding genes of formate dehydrogenase and hydrogenases presented higher abundances after microbial enrichment, which suggested that the enhancements of interspecies formate transfer and interspecies hydrogen transfer between syntrophic associations benefited volatile fatty acids (VFAs) conversion. This research provided an effective strategy to relieve acid accumulation.

Synthesis of Biogenic Palladium Nanoparticles Using Citrobacter sp. for Application as Anode Electrocatalyst in a Microbial Fuel Cell

Palladium (Pd) is a cheap and effective electrocatalyst that is capable of replacing platinum (Pt) in various applications. However, the problem in using chemically synthesized Pd nanoparticles (PdNPs) is that they are mostly fabricated using toxic chemicals under severe conditions. In this study, we present a more environmentally-friendly process in fabricating biogenic Pd nanoparticles (Bio-PdNPs) using Citrobacter sp. isolated from wastewater sludge. Successful fabrication of Bio-PdNPs was achieved under anaerobic conditions at pH six and a temperature of 30 °C using sodium formate (HCOONa) as an electron donor. Citrobacter sp. showed biosorption capabilities with no enzymatic contribution to Pd(II) uptake during absence of HCOONa in both live and dead cells. Citrobacter sp. live cells also displayed high enzymatic contribution to the removal of Pd(II) by biological reduction. This was confirmed by Scanning Electron Microscope (SEM), Electron Dispersive Spectroscopy (EDS), and X-ray Diffraction (XRD) characterization, which revealed the presence Bio-PdNPs deposited on the bacterial cells. The bio-PdNPs successfully enhanced the anode performance of the Microbial Fuel Cell (MFC). The MFC with the highest Bio-PdNPs loading (4 mg Bio-PdNP/cm2) achieved a maximum power density of 539.3 mW/m3 (4.01 mW/m2) and peak voltage of 328.4 mV.

Stabilization of Formate Dehydrogenase in a Metal-Organic Framework for Bioelectrocatalytic Reduction of CO2

The efficient fixation of excess CO₂ from the atmosphere to yield value-added chemicals remains crucial in response to the increasing levels of carbon emission. Coupling enzymatic reactions with electrochemical regeneration of cofactors is a promising technique for fixing CO₂ , while producing biomass which can be further transformed into biofuels. Herein, a bioelectrocatalytic system was established by depositing crystallites of a mesoporous metal-organic framework (MOF), termed NU-1006, containing formate dehydrogenase, on a fluorine-doped tin oxide glass electrode modified with Cp*Rh(2,2'-bipyridyl-5,5'-dicarboxylic acid)Cl₂ complex. This system converts CO₂ into formic acid at a rate of 79±3.4 mm h^-1 with electrochemical regeneration of the nicotinamide adenine dinucleotide cofactor. The MOF-enzyme composite exhibited significantly higher catalyst stability when subjected to non-native conditions compared to the free enzyme, doubling the formic acid yield.

Characterization of the protein fraction of the extracellular polymeric substances of three anaerobic granular sludges

Extracellular polymeric substances (EPS) play major roles in the efficacy of biofilms such as anaerobic granules, ranging from structural stability to more specific functions. The EPS of three granular anaerobic sludges of different origins were studied and compared. Particularly, the peptides from the protein fraction were identified by mass spectrometry. Desulfoglaeba and Treponema bacterial genera and Methanosaeta and Methanobacterium archaeal genera were prominent in all three sludges. Methanosaeta concilii proteins were the most represented in EPS of all three sludges studied. Principally, four proteins found in the three sludges, the S-layer protein, the CO-methylating acetyl-CoA synthase, an ABC transporter substrate-binding protein and the methyl-coenzyme M reductase, were expressed by Methanosaeta concilii. Mainly catabolic enzymes were found from the 45 proteins identified in the protein fraction of EPS. This suggests that EPS may have a role in allowing extracellular catabolic reactions.

Location controlled symmetry reduction: paradigm of an open metalloporphyrin framework based on the tetracarboxy porphyrin linker

The change in position of coordinating groups on symmetrical tetracarboxy porphyrin leads to novel class of reduced symmetry linker, which lay down pathway to obtain versatile coordination architectures to trap geometrically variant guest molecules.

A Review on Nanoparticles as Boon for Biogas Producers—Nano Fuels and Biosensing Monitoring

Nanotechnology has an increasingly large impact on a broad scope of biotechnological, pharmacological and pure technological applications. Its current use in bioenergy production from biomass is very restricted. The present study is based on the utilization of nanoparticles as an additive to feed bacteria that break down natural substances. The novel notion of dosing ions using modified nanoparticles can be used to progress up biogas production in oxygen free digestion processes. While minute nanoparticles are unstable, they can be designed to provide ions in a controlled approach, so that the maximum enhancement of biogas production that has been reported can be obtained. Nanoparticles are dissolved in a programmed way in an anaerobic atmosphere and are supplied in a sustainable manner to microbiotic organisms responsible for the degradation of organic material, which is a role that fits them well. Therefore, biogas fabrication can be increased up to 200%, thereby increasing the degradation of organic waste.

Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy

Hydrogenases are key enzymes of the energy metabolism of many microorganisms. Especially in anoxic habitats where molecular hydrogen (H₂) is an important intermediate, these enzymes are used to expel excess reducing power by reducing protons or they are used for the oxidation of H₂ as energy and electron source. Despite the fact that hydrogenases catalyze the simplest chemical reaction of reducing two protons with two electrons it turned out that they are often parts of multimeric enzyme complexes catalyzing complex chemical reactions with a multitude of functions in the metabolism. Recent findings revealed multimeric hydrogenases with so far unknown functions particularly in bacteria from the class Clostridia. The discovery of [FeFe] hydrogenases coupled to electron bifurcating subunits solved the enigma of how the otherwise highly endergonic reduction of the electron carrier ferredoxin can be carried out and how H₂ production from NADH is possible. Complexes of [FeFe] hydrogenases with formate dehydrogenases revealed a novel enzymatic coupling of the two electron carriers H₂ and formate. These novel hydrogenase enzyme complex could also contribute to biotechnological H₂ production and H₂ storage, both processes essential for an envisaged economy based on H₂ as energy carrier.

Toward a Hybrid Biosensor System for Analysis of Organic and Volatile Fatty Acids in Fermentation Processes

Monitoring of organic acids (OA) and volatile fatty acids (VFA) is crucial for the control of anaerobic digestion. In case of unstable process conditions, an accumulation of these intermediates occurs. In the present work, two different enzyme-based biosensor arrays are combined and presented for facile electrochemical determination of several process-relevant analytes. Each biosensor utilizes a platinum sensor chip (14 × 14 mm2) with five individual working electrodes. The OA biosensor enables simultaneous measurement of ethanol, formate, d- and l-lactate, based on a bi-enzymatic detection principle. The second VFA biosensor provides an amperometric platform for quantification of acetate and propionate, mediated by oxidation of hydrogen peroxide. The cross-sensitivity of both biosensors toward potential interferents, typically present in fermentation samples, was investigated. The potential for practical application in complex media was successfully demonstrated in spiked sludge samples collected from three different biogas plants. Thereby, the results obtained by both of the biosensors were in good agreement to the applied reference measurements by photometry and gas chromatography, respectively. The proposed hybrid biosensor system was also used for long-term monitoring of a lab-scale biogas reactor (0.01 m3) for a period of 2 months. In combination with typically monitored parameters, such as gas quality, pH and FOS/TAC (volatile organic acids/total anorganic carbonate), the amperometric measurements of OA and VFA concentration could enhance the understanding of ongoing fermentation processes.

Application of a Portable Multi-Analyte Biosensor for Organic Acid Determination in Silage

Multi-analyte biosensors may offer the opportunity to perform cost-effective and rapid analysis with reduced sample volume, as compared to electrochemical biosensing of each analyte individually. This work describes the development of an enzyme-based biosensor system for multi-parametric determination of four different organic acids. The biosensor array comprises five working electrodes for simultaneous sensing of ethanol, formate, d-lactate, and l-lactate, and an integrated counter electrode. Storage stability of the biosensor was evaluated under different conditions (stored at +4 °C in buffer solution and dry at −21 °C, +4 °C, and room temperature) over a period of 140 days. After repeated and regular application, the individual sensing electrodes exhibited the best stability when stored at −21 °C. Furthermore, measurements in silage samples (maize and sugarcane silage) were conducted with the portable biosensor system. Comparison with a conventional photometric technique demonstrated successful employment for rapid monitoring of complex media.

Discovery of a new metal and NAD+-dependent formate dehydrogenase from Clostridium ljungdahlii

Over the next decades, with the growing concern of rising atmospheric carbon dioxide (CO₂) levels, the importance of investigating new approaches for its reduction becomes crucial. Reclamation of CO₂ for conversion into biofuels represents an alternative and attractive production method that has been studied in recent years, now with enzymatic methods gaining more attention. Formate dehydrogenases (FDHs) are NAD(P)H-dependent oxidoreductases that catalyze the conversion of formate into CO₂ and have been extensively used for cofactor recycling in chemoenzymatic processes. A new FDH from Clostridium ljungdahlii (ClFDH) has been recently shown to possess activity in the reverse reaction: the mineralization of CO₂ into formate. In this study, we show the successful homologous expression of ClFDH in Escherichia coli. Biochemical and kinetic characterization of the enzyme revealed that this homologue also demonstrates activity toward CO₂ reduction. Structural analysis of the enzyme through homology modeling is also presented.

Hydrogenation of CO2 at ambient pressure catalyzed by a highly active thermostable biocatalyst

BACKGROUND

Replacing fossil fuels as energy carrier requires alternatives that combine sustainable production, high volumetric energy density, easy and fast refueling for mobile applications, and preferably low risk of hazard. Molecular hydrogen (H₂) has been considered as promising alternative; however, practical application is struggling because of the low volumetric energy density and the explosion hazard when stored in large amounts. One way to overcome these limitations is the transient conversion of H₂ into other chemicals with increased volumetric energy density and lower risk hazard, for example so-called liquid organic hydrogen carriers such as formic acid/formate that is obtained by hydrogenation of CO₂. Many homogenous and heterogenous chemical catalysts have been described in the past years, however, often requiring high pressures and temperatures. Recently, the first biocatalyst for this reaction has been described opening the route to a biotechnological alternative for this conversion.

RESULTS

The hydrogen-dependent CO₂ reductase (HDCR) is a highly active biocatalyst for storing H₂ in the form of formic acid/formate by reversibly catalyzing the hydrogenation of CO₂. We report the identification, isolation, and characterization of the first thermostable HDCR operating at temperatures up to 70 °C. The enzyme was isolated from the thermophilic acetogenic bacterium Thermoanaerobacter kivui and displays exceptionally high activities in both reaction directions, substantially exceeding known chemical catalysts. CO₂ hydrogenation is catalyzed at mild conditions with a turnover frequency of 9,556,000 h^-1 (specific activity of 900 µmol formate min^-1 mg^-1) and the reverse reaction, H₂ + CO₂ release from formate, is catalyzed with a turnover frequency of 9,892,000 h^-1 (930 µmol H₂ min^-1 mg^-1). The HDCR of T. kivui consists of a [FeFe] hydrogenase subunit putatively coupled to a tungsten-dependent CO₂ reductase/formate dehydrogenase subunit by an array of iron-sulfur clusters.

CONCLUSIONS

The discovery of the first thermostable HDCR provides a promising biological alternative for a chemically challenging reaction and might serve as model for the better understanding of catalysts able to efficiently reduce CO₂. The catalytic activity for reversible CO₂ hydrogenation of this enzyme is the highest activity known for bio- and chemical catalysts and requiring only ambient temperatures and pressures. The thermostability provides more flexibility regarding the process parameters for a biotechnological application.

The highly synergistic, broad spectrum, antibacterial activity of organic acids and transition metals

For millennia, transition metals have been exploited to inhibit bacterial growth. We report here the potentiation of the anti-bacterial activity of transition metals by organic acids. Strong synergy between low, non-toxic concentrations of transition metals and organic acids was observed with up to ~1000-fold higher inhibitory effect on bacterial growth. We show that organic acids shuttle transition metals through the permeability barrier of the bacterial membrane, leading to increased influx of transition metals into bacterial cells. We demonstrate that this synergy can be effectively used to inhibit the growth of a broad range of plant and human bacterial pathogens, and suggest that a revision of food preservation and crop protection strategies may be in order. These findings bear significant biomedical, agricultural, financial and environmental opportunities.

Development of a dye molecule-biocatalyst hybrid system with visible-light induced carbon–carbon bond formation from CO2 as a feedstock

Recently, CO₂ utilization technology, including artificial photosynthesis, has received much attention. In this field, CO₂ is used as a feedstock for fuels, polymers and in other chemical processes. Of note are malic enzymes (MEs) which catalyze the reaction of malic acid to pyruvic acid and CO₂ with the co-enzyme NADP⁺, and catalyze the reverse reaction of pyruvic acid and CO₂ to malic acid with the co-enzyme NADPH. Thus, MEs are also an attractive biocatalyst for carbon–carbon bond formation from CO₂. Studies of the visible light-induced malic acid production from pyruvic acid and CO₂ using an electron donor, a photosensitizer, an electron mediator, ferredoxin-NADP⁺ reductase, NADP⁺, and ME have been reported. However, modification of these systems is required, as they are very complicated. In this study, the visible light-induced carbon–carbon bond formation from pyruvic acid and CO₂ with ME using the photoreduction of 1,1′-diphenyl-4,4′-bipyridinium salt derivatives as a novel electron mediator with water-soluble tetraphenylporphyrin tetrasulfonate (H₂TPPS) in the presence of triethanolamine (TEOA) as an electron donor was developed. When a sample solution containing TEOA, H₂TPPS, 1,1′-diphenyl-4,4′-bipyridinium salt derivative, pyruvic acid, and ME in CO₂-saturated bis–tris buffer was irradiated, the major product was oxaloacetic acid. Thus, a visible light-induced photoredox system for carbon–carbon bond formation from CO₂ with ME using 1,1′-diphenyl-4,4′-bipyridinium salt derivative as an electron mediator was developed.

Hybrid photosynthesis-powering biocatalysts with solar energy captured by inorganic devices

The biological reduction of CO₂ driven by sunlight via photosynthesis is a crucial process for life on earth. However, the conversion efficiency of solar energy to biomass by natural photosynthesis is low. This translates in bioproduction processes relying on natural photosynthesis that are inefficient energetically. Recently, hybrid photosynthetic technologies with the potential of significantly increasing the efficiency of solar energy conversion to products have been developed. In these systems, the reduction of CO₂ into biofuels or other chemicals of interest by biocatalysts is driven by solar energy captured with inorganic devices such as photovoltaic cells or photoelectrodes. Here, we explore hybrid photosynthesis and examine the strategies being deployed to improve this biotechnology.

Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale

Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies.

Ruminal Fermentation of Anti-Methanogenic Nitrate- and Nitro-Containing Forages In Vitro

Nitrate, 3-nitro-1-propionic acid (NPA) and 3-nitro-1-propanol (NPOH) can accumulate in forages and be poisonous to animals if consumed in high enough amounts. These chemicals are also recognized as potent anti-methanogenic compounds, but plants naturally containing these chemicals have been studied little in this regard. Presently, we found that nitrate-, NPA-, or NPOH-containing forages effectively decreased methane production, by 35–87%, during in vitro fermentation by mixed cultures of ruminal microbes compared to fermentation by cultures incubated similarly with alfalfa. Methane production was further decreased during the incubation of mixed cultures also inoculated with Denitrobacterium detoxificans, a ruminal bacterium known to metabolize nitrate, NPA, and NPOH. Inhibition of methanogens within the mixed cultures was greatest with the NPA- and NPOH-containing forages. Hydrogen accumulated in all the mixed cultures incubated with forages containing nitrate, NPA or NPOH and was dramatically higher, exceeding 40 μmol hydrogen/mL, in mixed cultures incubated with NPA-containing forage but not inoculated with D. detoxificans. This possibly reflects the inhibition of hydrogenase-catalyzed uptake of hydrogen produced via conversion of 50 μmol added formate per milliliter to hydrogen. Accumulations of volatile fatty acids revealed compensatory changes in fermentation in mixed cultures incubated with the nitrate-, NPA-, and NPOH-containing forages as evidenced by lower accumulations of acetate, and in some cases, higher accumulations of butyrate and lower accumulations of ammonia, iso-buytrate, and iso-valerate compared to cultures incubated with alfalfa. Results reveal that nitrate, NPA, and NPOH that accumulate naturally in forages can be made available within ruminal incubations to inhibit methanogenesis. Further research is warranted to determine if diets can be formulated with nitrate-, NPA-, and NPOH-containing forages to achieve efficacious mitigation in ruminant methane emissions without adversely affecting fermentative efficiency or risking toxicity to animals.

Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate

Pyruvate formate-lyase (PFL) is a ubiquitous enzyme that supports increased ATP yield during sugar fermentation. While the PFL reaction is known to be reversible in vitro, the ability of PFL to support microbial growth by condensing acetyl-CoA and formate in vivo has never been directly tested. Here, we employ Escherichia coli mutant strains that cannot assimilate acetate via the glyoxylate shunt and use carbon labeling experiments to unequivocally demonstrate PFL-dependent co-assimilation of acetate and formate. Moreover, PFL-dependent growth is faster than growth on acetate using the glyoxylate shunt. Hence, growth via the reverse activity of PFL could have substantial ecological and biotechnological significance.

Formic acid as a hydrogen storage material – development of homogeneous catalysts for selective hydrogen release

Liquid energy: formic acid is an ideal candidate for catalytic release and storage of hydrogen.

The origin and evolution of ribonucleotide reduction

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B12-dependent mechanism in modern class II RNRs.

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO2, generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.

Metabolic engineering of carbon and redox flow in the production of small organic acids

The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high production and best compatibility with host physiology.

Efficient CO2-reducing activity of NAD-dependent formate dehydrogenase from Thiobacillus sp. KNK65MA for formate production from CO2 gas

NAD-dependent formate dehydrogenase (FDH) from Candida boidinii (CbFDH) has been widely used in various CO₂-reduction systems but its practical applications are often impeded due to low CO₂-reducing activity. In this study, we demonstrated superior CO₂-reducing properties of FDH from Thiobacillus sp. KNK65MA (TsFDH) for production of formate from CO₂ gas. To discover more efficient CO₂-reducing FDHs than a reference enzyme, i.e. CbFDH, five FDHs were selected with biochemical properties and then, their CO₂-reducing activities were evaluated. All FDHs including CbFDH showed better CO₂-reducing activities at acidic pHs than at neutral pHs and four FDHs were more active than CbFDH in the CO₂ reduction reaction. In particular, the FDH from Thiobacillus sp. KNK65MA (TsFDH) exhibited the highest CO₂-reducing activity and had a dramatic preference for the reduction reaction, i.e., a 84.2-fold higher ratio of CO₂ reduction to formate oxidation in catalytic efficiency (k_cat/K_B) compared to CbFDH. Formate was produced from CO₂ gas using TsFDH and CbFDH, and TsFDH showed a 5.8-fold higher formate production rate than CbFDH. A sequence and structural comparison showed that FDHs with relatively high CO₂-reducing activities had elongated N- and C-terminal loops. The experimental results demonstrate that TsFDH can be an alternative to CbFDH as a biocatalyst in CO₂ reduction systems.

Specific inhibitors for identifying pathways for methane production from carbon monoxide by a nonadapted anaerobic mixed culture

Specific inhibitors such as 2-bromoethanesulfonate (BES) and vancomycin were employed in activity batch tests to decipher metabolic pathways that are preferentially used by a mixed anaerobic consortium (sludge from an anaerobic digester) to transform carbon monoxide (CO) into methane (CH4). We first evaluated the inhibitory effect of both BES and vancomycin on the microbial community, as well as the efficiency and stability of vancomycin at 35 °C, over time. The activity tests with CO2-H2, CO, glucose, acetate, formate, propionate, butyrate, methanol, and ethanol showed that vancomycin does not inhibit some Gram-negative bacteria, and 50 mmol/L BES effectively blocks CH4 production in the sludge. However, when sludge was incubated with propionate, butyrate, methanol, or ethanol as the sole energy and carbon source, methanogenesis was only partially inhibited by BES. Separate tests showed that 0.07 mmol/L vancomycin is enough to maintain its inhibitory efficiency and stability in the population for at least 32 days at 35 °C. Using the inhibitors above, it was demonstrated that CO conversion to CH4 is an indirect, 2-step process, in which the CO is converted first to acetate and subsequently to CH4.

Interactions between microbial consortia in biofilms: a paradigm shift in rumen microbial ecology and enteric methane mitigation

Minimising enteric CH4 emissions from ruminants is a current research priority because CH4 contributes to global warming. The most effective mitigation strategy is to adjust the animal’s diet to complement locally available feed resources so that optimal production is gained from a minimum of animals. This essay concentrates on a second strategy – the use of feed additives that are toxic to methanogens or that redirect H2 (and electrons) to inhibit enteric CH4 emissions from individual animals. Much of the published research in this area is contradictory and may be explained when the microbial ecology of the rumen is considered. Rumen microbes mostly exist in organised consortia within biofilms composed of self-secreted extracellular polymeric substances attached to or within feed particles. In these biofilms, individual colonies are positioned to optimise their use of preferred intermediates from an overall process of organic matter fermentation that generates end-products the animal can utilise. Synthesis of CH4 within biofilms prevents a rise in the partial pressure of H2 (pH2) to levels that inhibit bacterial dehydrogenases, and so reduce fermentation rate, feed intake and digestibility. In this context, hypotheses are advanced to explain changes in hydrogen disposal from the biofilms in the rumen resulting from use of anti-methanogenic feed additives as follows. Nitrate acts as an alternative electron sink when it is reduced via NO2– to NH3 and CH4 synthesis is reduced. However, efficiency of CH4 mitigation is always lower than that predicted and decreases as NO3– ingestion increases. Suggested reasons include (1) variable levels of absorption of NO3–or NO2– from the rumen and (2) increases in H2 production. One suggestion is that NO3– reduction may lower pH2 at the surface of biofilms, thereby creating an ecological niche for growth of syntrophic bacteria that oxidise propionate and/or butyrate to acetate with release of H2. Chlorinated hydrocarbons also inhibit CH4 synthesis and increase H2 and formate production by some rumen methanogens. Formate diffuses from the biofilm and is converted to HCO3– and H2 in rumen fluid and is then excreted via the breath. Short-chain nitro-compounds inhibit both CH4 and formate synthesis when added to ruminal fluid but have little or no effect in redirecting H2 to other sinks, so the pH2 within biofilms may increase to levels that support reductive acetogenesis. Biochar or activated charcoal may also alter biofilm activity and reduce net CH4 synthesis; direct electron transfer between microbes within biofilms may also be involved. A final suggestion is that, during their sessile life stage, protozoa interact with biofilm communities and help maintain pH2 in the biofilm, supporting methanogenesis.