Metatranscriptomic Analysis Reveals the Coexpression of Hydrogen-Producing and Homoacetogenesis Genes in Dark Fermentative Reactors Operated at High Substrate Loads.

Microbial communities in dark fermentation continuous systems are affected by substrate type, concentration, and product accumulation (e.g., H2 and CO2). Metatranscriptomics and quantitative PCR (qPCR) were used to assess how high organic loading rates (OLR) from 60 to 160 g total carbohydrates (TC)/L-d modify the microbial community diversity and expression of key dark fermentative genes. Overall, the microbial communities were composed of H2-producing bacteria (Clostridium butyricum), homoacetogens (Clostridium luticellarii), and lactic acid bacteria (Enteroccocus gallinarum and Leuconostoc mesenteroides). Quantification through qPCR showed that the abundance of genes encoding the formyltetrahydrofolate synthetase (fthfs, homoacetogens) and hydrogenase (hydA, H2-producing bacteria) was strongly associated with the OLR and H2 production performance. Similarly, increasing the OLR influenced the abundance of the gene transcripts responsible for H2 production and homoacetogenesis. To evaluate the effect of decreasing the H2 partial pressure, silicone oil was added to the reactor at an OLR of 138 and 160 g TC/L-d, increasing the production of H2, the copies of genes codifying for hydA and fthfs, and the genes transcripts related to H2 production and homoacetogenesis. Moreover, the metatranscriptomic analysis also showed that lactate-type fermentation and dark fermentation simultaneously occurred without compromising the reactor performance for H2 production.

Knowing the enemy: homoacetogens in hydrogen production reactors.

One of the bottlenecks of the hydrogen production by dark fermentation is the low yields obtained because of the homoacetogenesis persistence, a metabolic pathway where H2 and CO2 are consumed to produce acetate. The central reactions of H2 production and homoacetogenesis are catalyzed by enzyme hydrogenase and the formyltetrahydrofolate synthetase, respectively. In this work, genes encoding for the formyltetrahydrofolate synthetase (fthfs) and hydrogenase (hydA) were used to investigate the diversity of homoacetogens as well as their phylogenetic relationships through quantitative PCR (qPCR) and next-generation amplicon sequencing. A total of 70 samples from 19 different H2-producing bioreactors with different configurations and operating conditions were analyzed. Quantification through qPCR showed that the abundance of fthfs and hydA was strongly associated with the type of substrate, organic loading rate, and H2 production performance. In particular, fthfs sequencing revealed that homoacetogens diversity was low with one or two dominant homoacetogens in each sample. Clostridium carboxivorans was detected in the reactors fed with agave hydrolisates; Acetobacterium woodii dominated in systems fed with glucose; Blautia coccoides and unclassified Sporoanaerobacter species were present in reactors fed with cheese whey; finally, Eubacterium limosum and Selenomonas sp. were co-dominant in reactors fed with glycerol. Altogether, quantification and sequencing analysis revealed that the occurrence of homoacetogenesis could take place due to (1) metabolic changes of H2-producing bacteria towards homoacetogenesis or (2) the displacement of H2-producing bacteria by homoacetogens. Overall, it was demonstrated that the fthfs gene was a suitable marker to investigate homoacetogens in H2-producing reactors. KEY POINTS: • qPCR and sequencing analysis revealed two homoacetogenesis phenomena. • fthfs gene was a suitable marker to investigate homoacetogens in H2 reactors.

Acetotrophic sulfate-reducing consortia develop active biofilms on zeolite and glass beads in batch cultures at initial pH 3.

Sulfate-reducing microbial communities remain a suitable option for the remediation of acid mine drainage using several types of carrier materials and appropriate reactor configurations. However, acetate prevails as a product derived from the incomplete oxidation of most organic substrates by sulfate reducers, limiting the efficiency of the whole process. An established sulfate-reducing consortium, able to degrade acetate at initial acidic pH (3.0), was used to develop biofilms over granular activated carbon (GAC), glass beads, and zeolite as carrier materials. In batch assays using glycerol, biofilms successfully formed on zeolite, glass beads, and GAC with sulfide production rates of 0.32, 0.26, and 0.14 mmol H2S/L·d, respectively, but only with glass beads and zeolite, acetate was degraded completely. The planktonic and biofilm communities were determined by the 16S rRNA gene analysis to evaluate the microbial selectivity of the carrier materials. In total, 46 OTUs (family level) composed the microbial communities. Ruminococcaceae and Clostridiaceae families were present in zeolite and glass beads, whereas Peptococcaceae was mostly enriched on zeolite and Desulfovibrionaceae on glass beads. The most abundant sulfate reducer in the biofilm of zeolite was Desulfotomaculum sp., while Desulfatirhabdium sp. abounded in the planktonic community. With glass beads, Desulfovibrio sp. dominated the biofilm and the planktonic communities. Our results indicate that both materials (glass beads and zeolite) selected different key sulfate-reducing microorganisms able to oxidize glycerol completely at initial acidic pH, which is relevant for a future application of the consortium in continuous bioreactors to treat acidic streams. KEY POINTS: • Complete consumption of glycerol and acetate at acidic pH by sulfate reduction. • Glass beads and zeolite are suitable materials to form sulfate-reducing biofilms. • Acetotrophic sulfate-reducing bacteria attached to zeolite preferably.

Continuous thermophilic hydrogen production from an enzymatic hydrolysate of agave bagasse: Inoculum origin, homoacetogenesis and microbial community analysis.

In this research, the performance of two thermophilic inocula of different origin on continuous hydrogen production from an enzymatic hydrolysate of agave bagasse were compared; one of them was obtained from a thermophilic reactor and the second one was taken from a mesophilic reactor and acclimated to thermophilic conditions. The acclimation process in one-step quickly established a high-performance hydrogen producing community, obtaining a volumetric hydrogen production rate of 3811 ± 19 mL H2/L-d with an hydrogen yield of 121 L H2/kg bagasse compared to 1473 ± 6 mL H2/L-d and 26.6 L H2/kg obtained with the thermophilic-origin inoculum. The differences in the performance of both inocula were closely linked to the profile of volatile fatty acids produced, the homoacetogenic pathway and the microbial community, the latter being the determining factor. The use of mesophilic-origin inoculum acclimated to thermophilic conditions can significantly improve the hydrogen production from lignocellulosic bagasse.

Standardized protocol for determination of biohydrogen potential.

Biohydrogen production potential (BHP) depends on several factors like inoculum source, substrate, pH, among many others. Batch assays are the most common strategy to evaluate such parameters, where the comparison is a challenging task due to the different procedures used. The present method introduces the first internationally validated protocol, evaluated by 8 independent laboratories from 5 different countries, to assess the biohydrogen potential. As quality criteria, a coefficient of variation of the cumulative hydrogen production (H max) was defined to be <15 %. Two options to run BHP batch tests were proposed; a manual protocol with periodic measurements of biogas production, needing conventional laboratory materials and analytical equipment for biogas characterization; and an automatic protocol, which is run in a device developed for online measurements of low biogas production. The detailed procedures for both protocol options are presented, as well as data validating them. The validation showed acceptable repeatability and reproducibility, measured as intra- and inter-laboratory coefficient of variation, which can be reduced up to 9 %.

Improvement of continuous hydrogen production using individual and binary enzymatic hydrolysates of agave bagasse in suspended-culture and biofilm reactors.

Continuous hydrogen (H2) production from individual (Stonezyme, IH) and binary (Celluclast-Viscozyme, BH) enzymatic hydrolysates of agave bagasse was evaluated in continuous stirred-tank reactors (CSTR) and trickling bed reactors (TBR). The volumetric H2 production rates (VHPR) in CSTR were 13 and 2.25 L H2/L-d with BH and IH, respectively. Meanwhile, VHPR of 5.76 and 2.0 L H2/L-d were obtained in the TBR configuration using BH and IH, respectively. Differences on VHPR between reactors could be explained by substrate availability, which is intrinsic to the growth mode of each reactor configuration; while differences of VHPR between hydrolysates were possibly related to the composition of enzymatic hydrolysates. Furthermore, homoacetogenesis was strongly influenced by H2 and substrate transfer conditions. Considering VHPR, H2 yields, and costs of hydrolysis, hydrogen production from binary hydrolysates of agave bagasse was identified as the most promising alternative evaluated with scale-up potential for the production of energy biofuels.

Hydrogen metabolic patterns driven by Clostridium-Streptococcus community shifts in a continuous stirred tank reactor.

The hydrogen (H2) production efficiency in dark fermentation systems is strongly dependent on the occurrence of metabolic pathways derived from the selection of microbial species that either consume molecular H2 or outcompete hydrogenogenic bacteria for the organic substrate. In this study, the effect of organic loading rate (OLR) on the H2 production performance, the metabolic pathways, and the microbial community composition in a continuous system was evaluated. Two bacterial genera, Clostridium and Streptococcus, were dominant in the microbial community depending on the OLR applied. At low OLR (14.7-44.1 gLactose/L-d), Clostridium sp. was dominant and directed the system towards the acetate-butyrate fermentation pathway, with a maximum H2 yield of 2.14 molH2/molHexose obtained at 29.4 gLactose/L-d. Under such conditions, the volumetric hydrogen production rate (VHPR) was between 3.2 and 11.6 LH2/L-d. In contrast, relatively high OLR (58.8 and 88.2 gLactose/L-d) favored the dominance of Streptococcus sp. as co-dominant microorganism leading to lactate production. Under these conditions, the formate production was also stimulated serving as a strategy to dispose the surplus of reduced molecules (e.g., NADH2+), which theoretically consumed up to 5.72 LH2/L-d. In such scenario, the VHPR was enhanced (13.7-14.5 LH2/L-d) but the H2 yield dropped to a minimum of 0.74 molH2/molHexose at OLR = 58.8 gLactose/L-d. Overall, this research brings clear evidence of the intrinsic occurrence of metabolic pathways detrimental for biohydrogen production, i.e., lactic acid fermentation and formate production, suggesting the use of low OLR as a strategy to control them.

Continuous hydrogen and methane production from Agave tequilana bagasse hydrolysate by sequential process to maximize energy recovery efficiency.

Continuous H2 and CH4 production in a two-stage process to increase energy recovery from agave bagasse enzymatic-hydrolysate was studied. In the first stage, the effect of organic loading rate (OLR) and stirring speed on volumetric hydrogen production rate (VHPR) was evaluated in a continuous stirred tank reactor (CSTR); by controlling the homoacetogenesis with the agitation speed and maintaining an OLR of 44 g COD/L-d, it was possible to reach a VHPR of 6 L H2/L-d, equivalent to 1.34 kJ/g bagasse. In the second stage, the effluent from CSTR was used as substrate to feed a UASB reactor for CH4 production. Volumetric methane production rate (VMPR) of 6.4 L CH4/L-d was achieved with a high OLR (20 g COD/L-d) and short hydraulic retention time (HRT, 14 h), producing 225 mL CH4/g-bagasse equivalent to 7.88 kJ/g bagasse. The two-stage continuous process significantly increased energy conversion efficiency (56%) compared to one-stage hydrogen production (8.2%).

Microbial communities from 20 different hydrogen-producing reactors studied by 454 pyrosequencing.

To provide new insight into the dark fermentation process, a multi-lateral study was performed to study the microbiology of 20 different lab-scale bioreactors operated in four different countries (Brazil, Chile, Mexico, and Uruguay). Samples (29) were collected from bioreactors with different configurations, operation conditions, and performances. The microbial communities were analyzed using 16S rRNA genes 454 pyrosequencing. The results showed notably uneven communities with a high predominance of a particular genus. The phylum Firmicutes predominated in most of the samples, but the phyla Thermotogae or Proteobacteria dominated in a few samples. Genera from three physiological groups were detected: high-yield hydrogen producers (Clostridium, Kosmotoga, Enterobacter), fermenters with low-hydrogen yield (mostly from Veillonelaceae), and competitors (Lactobacillus). Inocula, reactor configurations, and substrates influence the microbial communities. This is the first joint effort that evaluates hydrogen-producing reactors and operational conditions from different countries and contributes to understand the dark fermentation process.

Immobilization of biogenic Pd(0) in anaerobic granular sludge for the biotransformation of recalcitrant halogenated pollutants in UASB reactors.

The capacity of anaerobic granular sludge to reduce Pd(II), using ethanol as electron donor, in an upflow anaerobic sludge blanket (UASB) reactor was demonstrated. Results confirmed complete reduction of Pd(II) and immobilization as Pd(0) in the granular sludge. The Pd-enriched sludge was further evaluated regarding biotransformation of two recalcitrant halogenated pollutants: 3-chloro-nitrobenzene (3-CNB) and iopromide (IOP) in batch and continuous operation in UASB reactors. The superior removal capacity of the Pd-enriched biomass when compared with the control (not exposed to Pd) was demonstrated in both cases. Results revealed 80 % of IOP removal efficiency after 100 h of incubation in batch experiments performed with Pd-enriched biomass whereas only 28 % of removal efficiency was achieved in incubations with biomass lacking Pd. The UASB reactor operated with the Pd-enriched biomass achieved 81 ± 9.5 % removal efficiency of IOP and only 61 ± 8.3 % occurred in the control reactor lacking Pd. Regarding 3-CNB, it was demonstrated that biogenic Pd(0) promoted both nitro-reduction and dehalogenation resulting in the complete conversion of 3-CNB to aniline while in the control experiment only nitro-reduction was documented. The complete biotransformation pathway of both contaminants was proposed by high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis evidencing a higher degree of nitro-reduction and dehalogenation of both contaminants in the experiments with Pd-enriched anaerobic sludge as compared with the control. A biotechnological process is proposed to recover Pd(II) from industrial streams and to immobilize it in anaerobic granular sludge. The Pd-enriched biomass is also proposed as a biocatalyst to achieve the biotransformation of recalcitrant compounds in UASB reactors.

Recovery of palladium(II) by methanogenic granular sludge.

This is the first report that demonstrates the ability of anaerobic methanogenic granular sludge to reduce Pd(II) to Pd(0). Different electron donors were evaluated for their effectiveness in promoting Pd reduction. Formate and H2 fostered both chemically and biologically mediated Pd reduction. Ethanol only promoted the reduction of Pd(II) under biotic conditions and the reduction was likely mediated by H2 released from ethanol fermentation. No reduction was observed in biotic or abiotic assays with all other substrates tested (acetate, lactate and pyruvate) although a large fraction of the total Pd was removed from the liquid medium likely due to biosorption. Pd(II) displayed severe inhibition towards acetoclastic and hydrogenotrophic methanogens, as indicated by 50% inhibiting concentrations as low as 0.96 and 2.7 mg/L, respectively. The results obtained indicate the potential of utilizing anaerobic granular sludge bioreactor technology as a practical and promising option for Pd(II) reduction and recovery offering advantages over pure cultures.

Direct and quinone-mediated palladium reduction by Geobacter sulfurreducens: mechanisms and modeling.

Palladium(II) reduction to Pd(0) nanoparticles by Geobacter sulfurreducens was explored under conditions of neutral pH, 30 °C and concentrations of 25, 50, and 100 mg of Pd(II)/L aiming to investigate the effect of solid species of palladium on their microbial reduction. The influence of anthraquinone-2,6-disulfonate was reported to enhance the palladium reaction rate in an average of 1.7-fold and its addition is determining to achieve the reduction of solid species of palladium. Based on the obtained results two mechanisms are proposed: (1) direct, which is fully described considering interactions of amide, sulfur, and phosphoryl groups associated to proteins from bacteria on palladium reduction reaction, and (2) quinone-mediated, which implies multiheme c-type cytochromes participation. Speciation analysis and kinetic results were considered and integrated into a model to fit the experimental data that explain both mechanisms. This work provides elements for a better understanding of direct and quinone-mediated palladium reduction by G. sulfurreducens, which could facilitate metal recovery with concomitant formation of valuable palladium nanoparticles in industrial processes.

Biotic and abiotic characterization of bioanodes formed on oxidized carbon electrodes as a basis to predict their performance.

Bioelectrochemical systems (BESs) are based on the catalytic activity of biofilm on electrodes, or the so-called bioelectrodes, to produce electricity and other valuable products. In order to increase bioanode performance, diverse electrode materials and modification methods have been implemented; however, the factors directly affecting performance are yet unclear. In this work carbon cloth electrodes were modified by thermal, chemical, and electrochemical oxidation to enhance oxygenated surface groups, to modify the electrode texture, and consequently the electron transfer rate and biofilm adhesion. The oxidized electrodes were physically, chemically, and electrochemically characterized, then bioanodes were formed at +0.1 V vs. Ag/AgCl using domestic wastewater amended with acetate. The bioanode performance was evaluated according to the current and charge generated. The efficacy of the treatments were in the order Thermal>Electrochemical>Untreated>Chemical oxidation. The maximum current observed with untreated electrode was 0.152±0.026 mA (380±92 mA m(-2)), and it was increased by 78% and 28% with thermal and electrochemical oxidized electrodes, respectively. Moreover, the volatile solids correlated significantly with the maximum current obtained, and the electrode texture was revealed as a critical factor for increasing the bioanode performance.

Maximizing hydrogen production and substrate consumption by Escherichia coli WDHL in cheese whey fermentation.

Fermentative hydrogen production is strongly affected by pH. In order to maximize hydrogen production and substrate consumption in Escherichia coli ΔhycA, ΔlacI (WDHL) cheese whey fermentation, the influence of pH control at values of 5.5, 6, and 6.5 was studied in batch stirred-tank bioreactors. From the conditions evaluated, pH 6.5 was the best condition, at which the highest cumulative hydrogen production and yield (1.78 mol H2/mol lactose) were obtained. Moreover, at this pH, all carbohydrates from the cheese whey were consumed, and a mix of ethanol and organic acids, mainly lactate, were produced from glucose, whereas galactose yielded acetate, ethanol, and succinate. Operating the reactor at pH 5.5 resulted in the highest maximum specific production rate, but smaller hydrogen yield because only glucose was metabolized and galactose was accumulated. At pH 6, not all cheese whey carbohydrates were consumed, and it was not favorable for hydrogen production. Lactose consumption and growth kinetics were not affected by the pH. The results show the importance of controlling pH to maximize hydrogen production and substrate consumption using cheese whey as substrate.

Arsenic mobility controlled by solid calcium arsenates: a case study in Mexico showcasing a potentially widespread environmental problem.

An As-contaminated perched aquifer under an urban area affected by mining was studied over a year to determine the contamination source species and the mechanism of As mobilization. Results show that the dissolution of calcium arsenates in residues disposed on an inactive smelter has caused high levels of As pollution in the adjoining downgradient 6-km perched aquifer, reaching up to 158 mg/L of dissolved As, and releasing a total of ca. 7.5 tons of As in a year. Furthermore, free calcium ion availability was found to control As mobility in the aquifer through the diagenetic precipitation of calcium arsenates (Ca5H2(AsO4)4·cH2O) preventing further mobilization of As. Results shown here represent a model for understanding a highly underreported mechanism of retention of arsenate species likely to dominate in calcium-rich environments, such as those in calcareous sediments and soils, where the commonly reported mechanism of adsorption to iron(III) oxyhydroxides is not the dominant process.

Reduction of palladium and production of nano-catalyst by Geobacter sulfurreducens.

The present study is the first report on the ability of Geobacter sulfurreducens PCA to reduce Pd(II) and produce Pd(0) nano-catalyst, using acetate as electron donor at neutral pH (7.0 ± 0.1) and 30 °C. The microbial production of Pd(0) nanoparticles (NPs) was greatly enhanced by the presence of the redox mediator, anthraquinone-2,6-disulfonate (AQDS) when compared with controls lacking AQDS and cell-free controls. A cell dry weight (CDW) concentration of 800 mg/L provided a larger surface area for Pd(0) NPs deposition than a CDW concentration of 400 mg/L. Sample analysis by transmission electron microscopy revealed the formation of extracellular Pd(0) NPs ranging from 5 to 15 nm and X-ray diffraction confirmed the Pd(0) nature of the nano-catalyst produced. The present findings open the possibility for a new alternative to synthesize Pd(0) nano-catalyst and the potential application for microbial metal recovery from metal-containing waste streams.

Distribution of CO(2) fixation and acetate mineralization pathways in microorganisms from extremophilic anaerobic biotopes.

Extremophilic anaerobes are widespread in saline, acid, alkaline, and high or low temperature environments. Carbon is essential to living organisms and its fixation, degradation, or mineralization is driven by, up to now, six metabolic pathways. Organisms using these metabolisms are known as autotrophs, acetotrophs or carbon mineralizers, respectively. In anoxic and extreme environments, besides the well-studied Calvin-Benson-Bassham cycle, there are other five carbon fixation pathways responsible of autotrophy. Moreover, regarding carbon mineralization, two pathways perform this key process for carbon cycling. We might imagine that all the pathways can be found evenly distributed in microbial biotopes; however, in extreme environments, this does not occur. This manuscript reviews the most commonly reported anaerobic organisms that fix carbon and mineralize acetate in extreme anoxic habitats. Additionally, an inventory of autotrophic extremophiles by biotope is presented.

Chemical and enzymatic sequential pretreatment of oat straw for methane production.

Oat straw was subjected to sequential pretreatment: acid/alkaline/enzymatic, to convert the lignocellulosic material in soluble sugars. The hydrolysates from acid pretreatment (2% HCl, 90 °C) and enzymatic pretreatment (cellulase, pH 4.5, 45 °C) were used as substrates in two lab-scale UASB reactors for methane production. The acid and enzymatic hydrolysates contained 25.6 and 35.3g/L of total sugars, respectively, which corresponded to a COD of 23.6 and 30.5 g/L, respectively. The UASB reactor fed with acid hydrolysate achieved a maximum methane yield of 0.34 L CH(4)/g COD at an organic loading rate (OLR) of 2.5 g COD/L-d. In the reactor fed with enzymatic hydrolysate the methane yield was 0.36 LCH(4)/g COD at OLR higher than 8.8 g COD/L-d. The anaerobic digestion of both hydrolysates was feasible without the need of a detoxification step. The sequential pretreatment of oat straw allowed to solubilize 96.8% of hemicellulose, 77.2% of cellulose and 42.2% of lignin.

Fermentation of lactose and its constituent sugars by Escherichia coli WDHL: impact on hydrogen production.

Fermentations of lactose, glucose and galactose using Escherichia coli WDHL, a hydrogen over producer strain, were performed. With glucose as substrate pyruvate was mainly routed to the lactate pathway, resulting in hydrogen production and yield of 1037 mL and 0.30 mol H(2)/mol of glucose, respectively. When galactose was the substrate, the pyruvate formate lyase pathway was the main route for pyruvate and a fermentation yield of 1.12 mol H(2)/mol of galactose and a hydrogen production of 2080 mL were obtained. The fermentation of lactose or glucose plus galactose showed a similar yield of 1.02 mol H(2)/mol of hexose consumed. This work clearly demonstrated that the kinetics of hydrogen and metabolites production as well as the hydrogen yield were affected by the type of sugar used as substrate as reflected by the deviations from the metabolic hydrogen-production pathway.

Inhibition of sulfate reduction by iron, cadmium and sulfide in granular sludge.

This study investigated the inhibition effect of iron, cadmium and sulfide on the substrate utilization rate of sulfate reducing granular sludge. A series of batch experiments in a UASB reactor were conducted with different concentrations of iron (Fe2+, 4.0-8.5 mM), cadmium (Cd2+, 0.53-3.0 mM) and sulfide (4.2-10.6 mM), the reactor was fed with ethanol at 1g chemical oxygen demand (COD)/L and sulfate to yield a COD/SO4(2-) (g/g) ratio of 0.5. The addition of iron, up to a concentration of 8.1mM, had a positive effect on the substrate utilization rate which increased 40% compared to the rate obtained without metal addition (0.25 g COD/gVSS-d). Nonetheless, iron concentration of 8.5 mM inhibited the specific substrate utilization rate by 57% compared to the substrate utilization rate obtained in the batch amended with 4.0 mM Fe2+ (0.44 g COD/gVSS-d). Cadmium had a negative effect on the specific substrate utilization rate at the concentrations tested; at 3.0 mM Cd2+ the substrate utilization rate was inhibited by 44% compared with the substrate utilization rate without metal addition. Cadmium precipitation with sulfide did not decrease the inhibition of cadmium on sulfate reduction. These results could have important practical implications mainly when considering the application of the sulfate reducing process to treat effluents with high concentrations of sulfate and dissolved metals such as iron and cadmium.