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.

The key role of biogenic arsenic sulfides in the removal of soluble arsenic and propagation of arsenic mineralizing communities.

Biogeochemical processes govern the transport and availability of arsenic in sediments. However, little is known about the transition from indigenous communities to cultivable consortia when exposed to high arsenic concentrations. Such cultivable communities could be exploited for arsenic bioremediation of waste streams and polluted sites. Thus, it is crucial to understand the dynamics and selective pressures that shape the communities during the development of customized bacterial consortia. First, from the arsenic partitioning of two sediments with high arsenic concentrations, we found that up to 55% of arsenic was bioavailable because it was associated with the soluble, carbonate, and ionically exchangeable fractions. Next, we prepared sediment enrichment cultures under arsenate- and sulfate-reducing conditions to precipitate arsenic sulfide biominerals and analyze the communities. The produced biominerals were used as the inoculum to develop bacterial consortia via successive transfers. Tracking of the 16S rRNA gene in the fresh sediments, sediment enrichments, biogenic minerals, and bacterial consortia revealed differences in the bacterial communities. Removing the sediment caused a substantial decrease in diversity and shifts toward the dominance of the Firmicutes phylum to the detriment of Proteobacteria. In agreement with the 16S rRNA gene results, the sequencing of the arrA gene confirmed the presence of phylotypes closely related to Desulfosporosinus sp. Y5 (100% similarity), highlighting the pivotal role of this genus in the removal of soluble arsenic. Here, we demonstrated for the first time that besides being important as arsenic sinks, the biogenic arsenic sulfide minerals are reservoirs of arsenic resistant/respiring bacteria and can be used to culture them.

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.

Author Correction: Improving Substrate Consumption and Decrease of Growth Yield in Aerobic Cultures of Pseudomonas denitrificans By Applying Low Voltages in Bioelectric Systems.

The original version of this article unfortunately contained a mistake in Equation 1.

Improving Substrate Consumption and Decrease of Growth Yield in Aerobic Cultures of Pseudomonas denitrificans By Applying Low Voltages in Bioelectric Systems.

It is well known that activated sludge treatment systems generate a lot of surplus sludge having environmental and economic impacts. Although several approaches have been proposed for the treatment/reuse of the excess of sludge, there are few studies focused on decreasing the biomass yield without affecting the metabolic activity. This work reports the effect of low magnitude electrical fields (0.07 to 0.2 V/cm) on the growth yield of a pure strain of Pseudomonas denitrificans (used as model microorganism). Cell potentials between 0.2 and 0.57 V were measured during 24 h to the aerobic culture; biomass production and substrate consumption were evaluated at regular intervals. Results indicated that the substrate (lactate) consumption efficiency increased with the applied potential, up to 100%, while the yield diminished 31% (0.34 g biomass/g lactate consumed) at 0.7 V vs. NHE. Bioenergetics showed that the fraction of electron equivalents toward biomass synthesis decreased from 0.68 (when no potential was applied) to 0.47 at 0.57 V, pointing out the redirection of the energy flow toward maintenance to cope with the stress caused by the imposed voltage. Therefore, the electrical stimulus could be used as control of biomass growth in aerobic wastewater treatment lines.

Dissolution and final fate of arsenic associated with gypsum, calcite, and ferrihydrite: Influence of microbial reduction of As(V), sulfate, and Fe(III).

Several studies have demonstrated that gypsum (CaSO4·2H2O) and calcite (CaCO3) can be important hosts of arsenic in contaminated hydrogeological systems. However, the extent to which microbial reducing processes contribute to the dissolution and transformation of carbonate and sulfate minerals and, thereby, to arsenic mobilization is poorly understood. These processes are likely to have a strong impact on arsenic mobility in iron-poor environments and in reducing aquifers where iron oxyhydroxides become unstable. Anoxic batch bioassays with arsenate (As(V)) coprecipitated with calcite, gypsum, or ferrihydrite (Fe(OH)3) were conducted in the presence of sulfate or molybdate to examine the impact of bioprocesses (i.e. As(V), sulfate, and Fe(III)-reduction) on arsenic dissolution, speciation, and eventual remineralization. Microbial reduction of As(V)-bearing calcite caused an important dissolution of arsenite, As(III), which remained in solution up to the end of the experiment (30 days). The reduction of As(V) from gypsum-As(V) also led to the release of As(III), which was subsequently remineralized, possibly as arsenic sulfides. The presence of sulfate triggered arsenic dissolution in the bioassays with ferrihydrite-As(V). This study showed that although gypsum and calcite have a lower capacity to bind arsenic, compared to iron oxides, they can play a critical role in the biogeochemical cycle of arsenic in natural calcareous and gypsiferous systems depleted of iron since they can be a source of electron acceptors for reducing bioprocesses.

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.

Role of indigenous microbiota from heavily contaminated sediments in the bioprecipitation of arsenic.

High arsenic concentrations have been detected in alluvial aquifers of arid and semi-arid zones in Mexico. This work describes the potential of microbial arsenate reduction of the indigenous community present in sediments from an arsenic contaminated aquifer. Microcosms assays were conducted to evaluate arsenate and sulfate-reducing activities of the native microbiota. Two different sediments were used as inoculum in the assays amended with lactate (10mM) as electron donor and with sulfate and arsenate (10mM each) as electron acceptors. Sediments were distinguished by their concentration of total arsenic 238.3±4.1mg/kg or 2263.1±167.7mg/kg, which may be considered as highly contaminated sediments with arsenic. Microbial communities present in both sediments were able to carry out arsenate reduction, accomplished within 4days, with the corresponding formation of arsenite; sulfate reduction took place as well. Both reducing activities occurred without previous acclimation period or enrichment, even at potential inhibitory concentrations of arsenate as high as 750mg/L (10mM). The formation of a yellowish colloidal precipitate was evident when both reducing processes occurred in the microcosm, which contributed to remove between 52 and 90.9% of As(III) from the liquid phase by bioprecipitation of arsenic as arsenic sulfide.

Graphene oxide as electron shuttle for increased redox conversion of contaminants under methanogenic and sulfate-reducing conditions.

Graphene oxide (GO) is reported for the first time as electron shuttle to increase the redox conversion of the azo compound, reactive red 2 (RR2, 0.5mM), and the nitroaromatic, 3-chloronitrobenzene (3CNB, 0.5mM). GO (5mgL(-1)) increased 10-fold and 7.6-fold the reduction rate of RR2 and 3CNB, respectively, in abiotic incubations with sulfide (2.6mM) as electron donor. GO also increased by 2-fold and 3.6-fold, the microbial reduction rate of RR2 by anaerobic sludge under methanogenic and sulfate-reducing conditions, respectively. Deep characterization of GO showed that it has a proper size distribution (predominantly between 450 and 700nm) and redox potential (+50.8mV) to promote the reduction of RR2 and 3CNB. Further analysis revealed that biogenic sulfide plays a major role on the GO-mediated reduction of RR2. GO is proposed as an electron shuttle to accelerate the redox conversion of recalcitrant pollutants, such as nitro-benzenes and azo dyes.

Humus-reducing microorganisms and their valuable contribution in environmental processes.

Humus constitutes a very abundant class of organic compounds that are chemically heterogeneous and widely distributed in terrestrial and aquatic environments. Evidence accumulated during the last decades indicating that humic substances play relevant roles on the transport, fate, and redox conversion of organic and inorganic compounds both in chemically and microbially driven reactions. The present review underlines the contribution of humus-reducing microorganisms in relevant environmental processes such as biodegradation of recalcitrant pollutants and mitigation of greenhouse gases emission in anoxic ecosystems, redox conversion of industrial contaminants in anaerobic wastewater treatment systems, and on the microbial production of nanocatalysts and alternative energy sources.

Immobilized humic substances as redox mediator for the simultaneous removal of phenol and Reactive Red 2 in a UASB reactor.

The present study reports a novel treatment concept combining the redox-mediating capacity of immobilized humic substances with the biodegrading activity of anaerobic sludge for the simultaneous removal of two representative pollutants of textile wastewaters (e.g., phenol and Reactive Red 2 (RR2)) in a high-rate anaerobic reactor. The use of immobilized humic substances (1 g total organic carbon (TOC) L(-1), supported on an anion exchange resin) in an upflow anaerobic sludge blanket (UASB) reactor increased the decolorization efficiency of RR2 (~90 %), extent of phenol oxidation (~75 %), and stability as compared to a control UASB reactor operated without immobilized humic substances, which collapsed after 120 days of dye introduction (50-100 mg L(-1)). Increase in the concentration of immobilized humic substances (2 g TOC L(-1)) further enhanced the stability and efficiency of the UASB reactor. Detection of aniline in the effluent as RR2 reduction product confirmed that reduction of RR2 was the major mechanism of dye removal. This is the first demonstration of immobilized humic substances serving as effective redox mediators for the removal of recalcitrant pollutants from wastewater in a high-rate anaerobic bioreactor. The novel treatment concept could also be applicable to remove a wide variety of contaminants susceptible to redox conversion, which are commonly found in different industrial sectors.

Enhanced microbial decolorization of methyl red with oxidized carbon fiber as redox mediator.

The anaerobic degradation of azo dyes under anaerobic conditions is possible but at a slow rate. Redox mediators (quinones, activated carbon) are used to improve the reduction rate. The aim of this work was to use activated carbon fiber (ACF) as a redox mediator for the anaerobic reduction of the azo dye methyl red. ACF was chemically modified with 8M HNO3 to increase its redox-mediating capacity and used in chemical and anaerobic biological batch assays for the reduction of methyl red. ACF increased its redox-mediating capacity up to 3-fold in chemical assays; in biological assays ACF increased the reduction rate up to 8-fold compared to controls without ACF. However, since the ACF served as support for biomass, a biofilm formed on the fiber significantly reduced its redox-mediating capacity; substrate consumption suggested that the electron transport from ACF to methyl red was the rate-limiting step in the process. These results are the first evidence of the role of ACF as a redox mediator in the reductive decolorization of methyl red, in addition to the effect of biofilm attached to ACF on methyl red reduction. Due to the versatile characteristics of ACF and its redox-mediating capacity, carbon fibers could be used in biological wastewater treatment systems to accelerate the reductive transformation of pollutants commonly found in industrial effluents.

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.

Phylogenetic diversity of methyl-coenzyme M reductase (mcrA) gene and methanogenesis from trimethylamine in hypersaline environments.

Methanogens have been reported in complex microbial communities from hypersaline environments, but little is known about their phylogenetic diversity. In this work, methane concentrations in environmental gas samples were determined while methane production rates were measured in microcosm experiments with competitive and non-competitive substrates. In addition, the phylogenetic diversity of methanogens in microbial mats from two geographical locations was analyzed: the well studied Guerrero Negro hypersaline ecosystem, and a site not previously investigated, namely Laguna San Ignacio, Baja California Sur, Mexico. Methanogenesis in these microbial mats was suspected based on the detection of methane (in the range of 0.00086 to 3.204 %) in environmental gas samples. Microcosm experiments confirmed methane production by the mats and demonstrated that it was promoted only by non-competitive substrates (trimethylamine and methanol), suggesting that methylotrophy is the main characteristic process by which these hypersaline microbial mats produce methane. Phylogenetic analysis of amino acid sequences of the methyl coenzyme-M reductase (mcrA) gene from natural and manipulated samples revealed various methylotrophic methanogens belonging exclusively to the family Methanosarcinaceae. Moderately halophilic microorganisms of the genus Methanohalophilus were predominant (>60 % of mcrA sequences retrieved). Slightly halophilic and marine microorganisms of the genera Methanococcoides and Methanolobus, respectively, were also identified, but in lower abundances.

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.

Inhibitory concentrations of 2,4D and its possible intermediates in sulfate reducing biofilms.

Different concentrations of the herbicide 2,4-dichlorophenoxyacetic acid (2,4D) and its possible intermediates such as 2,4-dichlorophenol (2,4DCP), 4-chlorophenol (4CP), 2-chlorophenol (2CP) and phenol, were assayed to evaluate the inhibitory effect on sulfate and ethanol utilization in a sulfate reducing biofilm. Increasing concentrations of the chlorophenolic compounds showed an adverse effect on sulfate reduction rate and ethanol conversion to acetate, being the intermediate 2,4DCP most toxic than the herbicide. The monochlorophenol 4CP (600 ppm) caused the complete cessation of sulfate reduction and ethanol conversion. The ratio of the electron acceptor to the electron donor utilized as well as the sulfate utilization volumetric rates, diminished when chlorophenols and phenol concentrations were increased, pointing out to the inhibition of the respiratory process and electrons transfer. The difference found in the IC(50) values obtained was due to the chemical structure complexity of the phenolic compounds, the number of chlorine atoms as much as the chlorine atom position in the phenol ring. The IC(50) values (ppm) indicated that the acute inhibition on the biofilm was caused by 2,4DCP (17.4) followed by 2,4D (29.0), 2CP (99.8), 4CP (108.0) and phenol (143.8).

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.

Characterization of sulfate-reducing bacteria dominated surface communities during start-up of a down-flow fluidized bed reactor.

An anaerobic down-flow fluidized bed reactor was inoculated with granular sludge and started-up with sulfate containing synthetic wastewater to promote the formation of a biofilm enriched in sulfate-reducing bacteria (SRB), to produce biogenic sulfide. The start-up was done in two stages operating the reactor in batch for 45 days followed by 85 days of continuous operation. Low-density polyethylene was used as support. The biofilm formation was followed up by biochemical and electron microscopy analyses and the composition of the community was examined by 16S rDNA sequence analysis. Maximum immobilized volatile solids (1.2 g IVS/L(support)) were obtained after 14 days in batch regime. During the 85 days of continuous operation, the reactor removed up to 80% of chemical oxygen demand (COD), up to 28% of the supplied sulfate and acetate was present in the effluent. Sulfate-reducing activity determined in the biofilm with ethanol or lactate as substrate was 11.7 and 15.3 g COD/g IVS per day, respectively. These results suggested the immobilization of sulfate reducers that incompletely oxidize the substrate to acetate; the phylogenetic analysis of the cloned 16S rDNA gene sequences showed high identity to the genus Desulfovibrio that oxidizes the substrates incompletely. In contrast, in the granular sludge used as inoculum a considerable number of clones showed homology to Methanobacterium and just few clones were close to SRB. The starting-up approach allowed the enrichment of SRB within the diverse community developed over the polyethylene support.

Precipitation and recovery of metal sulfides from metal containing acidic wastewater in a sulfidogenic down-flow fluidized bed reactor.

This study reports the feasibility of recovering metal precipitates from a synthetic acidic wastewater containing ethanol, Fe, Zn, and Cd at an organic loading rate of 2.5 g COD/L-day and a COD to sulfate ratio of 0.8 in a sulfate reducing down-flow fluidized bed reactor. The metals were added at increasing loading rates: Fe from 104 to 320 mg/L-day, Zn from 20 to 220 mg/L-day, and Cd from 5 to 20 mg/L-day. The maximum COD and sulfate removals attained were 54% and 41%, respectively. The biofilm reactor was operated at pH as low as 5.0 with stable performance, and no adverse effect over COD consumption or sulfide production was observed. The metals precipitation efficiencies obtained for Fe, Zn, and Cd exceeded 99.7%, 99.3%, and 99.4%, respectively. The total recovered precipitate was estimated to be 90% of the theoretical mass expected as metal sulfides. The precipitate was mainly recovered from the bottom of the reactor and the equalizer. The analysis of the precipitates showed the presence of pyrite (FeS2), sphalerite (ZnS) and greenockite (CdS); no metal hydroxides or carbonates in crystalline phases were identified. This study is the first in reporting the feasibility to recover metal sulfides separated from the biomass in a sulfate reducing process in one stage.