Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H2-coproducing system, analyzed using the [Fe]-hydrogenase gene

Harnessing Nanomaterials for Enhanced Biohydrogen Generation from Wastewater

Biohydrogen is considered a green fuel due to its eco-friendly nature since it only produces water and energy on combustion. However, their lower yield and production rate is one of the foremost challenges that need an instant sustainable approach. The use of nanotechnology is a potential approach for the enhanced generation of biohydrogen, owing to the significant characteristics of the nanomaterials such as greater specificity, high surface-area-to-volume ratio, better reactivity and dispersibility, enhanced catalytic activity, superb selectivity, greater electron transfer, and better anaerobic microbiota activity. This article explores the recent trends and innovations in the production of biohydrogen from wastewater through the applications of different nanomaterials. The potential of various nanomaterials employed for biohydrogen production from wastewater is evaluated and the impacts of important parameters such as the concentration and size of the nanomaterials, temperature, and pH on the production and yield of biohydrogen are explained in detail. Several pathways involved in the mechanistic approach of biohydrogen generation from wastewater are critically assessed. Lastly, numerous technological challenges are highlighted and recommendations regarding future research are also provided.

Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber

Microplastic (MP) is an environmental burden and enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. Isopods represent ubiquitously abundant, ecologically important detritivores. However, MP-polymer specific effects on the host and its gut microbiota are unknown. We tested the hypothesis that biodegradable (polylactic acid [PLA]) and non-biodegradable (polyethylene terephthalate [PET]; polystyrene [PS]) MPs have contrasting effects on P. scaber mediated by changes of the gut microbiota. The isopod fitness after an 8-week MP-exposure was generally unaffected, although the isopods showed avoidance behaviour to PS-food. MP-polymer specific effects on gut microbes were detected, including a stimulation of microbial activity by PLA compared with MP-free controls. PLA stimulated hydrogen emission from isopod guts, while PET and PS were inhibitory. We roughly estimated 107  kg year-1 hydrogen emitted from the isopods globally and identified their guts as anoxic, significant mobile sources of reductant for soil microbes despite the absence of classical obligate anaerobes, likely due to Enterobacteriaceae-related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of important isopod hydrogen emissions by MP pollution and the potential of MP to affect terrestrial food webs.

Promotion of biological H2 (Bio-H2) production by the nitrogen-fixing anaerobic microbial consortia using humin, a solid-phase humic substance

Dark fermentative biological hydrogen (Bio-H₂) production is expected to be a clean and sustainable H₂ production technology, and the technologies have been studied to increase in the product yield as index. This study achieved high product yields of Bio-H₂ using nitrogen-fixing consortia under nitrogen-deficient conditions with glucose or mannitol as substrate and humin as the extracellular electron mediator: 4.12 mol-H₂/mol-glucose and 3.12 mol-H₂/mol-mannitol. The high Bio-H₂ production was observed under the conditions where both nitrogenase and hydrogenase were active in the presence of humin. Nitrogenase activity was confirmed by acetylene reduction activity and hydrogenase activity by Bio-H₂ production under nitrogenase-inhibiting conditions with NH₄NO₃. [Fe-Fe] hydrogenase detected by a specific PCR and acetate, butyrate, formate, lactate, and pyruvate produced as by-products suggested the involvement of both pyruvate-ferredoxin-oxidoreductase and pyruvate formate lyase pathways in Bio-H₂ production. Humin promoted the Bio-H₂ production beyond the capacity of the consortium, which had reached saturation with the optimum concentrations of glucose and mannitol. Carbon balance suggested the concurrent H₂ consumption by hydrogenotrophic methanogenesis and acetogenesis. Bio-H₂ production of the washed and starved consortium with reduced humin under conditions with or without NH₄NO₃ suggests that humin promoted hydrogenase and nitrogenase activity by donating extracellular electrons. Clostridium and Ruminococcus in the consortia were considered major hydrogen producers. Thus, this study demonstrated the outstanding potential of nitrogen-fixing consortia under nitrogen-deficient conditions with humin as an extracellular electron mediator for dark fermentative Bio-H₂ production with high yields.

Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

Molecular mechanism of ethanol-H2 co-production fermentation in anaerobic acidogenesis: Challenges and perspectives

Ethanol-type fermentation (ETF) is one of three fermentation types during the acidogenesis of the anaerobic biological treatment. Ethanoligenens, a representative genus of ETF, displays acidophilic, autoaggregative, and ethanol-H₂ co-producing characteristics and facilitates subsequent methanogenesis. Here, the latest advances in the molecular mechanisms of the metabolic regulation of ethanol-H₂ co-producing bacteria based on multi-omics studies were comprehensively reviewed. Comparative genomics demonstrated a low genetic similarity between Ethanoligenens and other hydrogen-producing genera. FeFe‑hydrogenases (FeFe-H₂ases) and pyruvate ferredoxin oxidoreductase (PFOR) played critical roles in the ethanol-H₂ co-metabolic pathway of Ethanoligenens. Global transcriptome analysis revealed that highly expressed [FeFe]-H₂ases and ferredoxins drove hydrogen production by Ethanoligenens at low pH conditions (4.0-4.5). Quantitative proteomic analysis also proved that this genus resists acetic acid-induced intracellular acidification through the up-regulated expression of pyrimidine metabolism related proteins. The autoaggregation of Ethanoligenen facilitated its granulation with acetate-oxidizing bacteria in co-culture systems and mitigated a fast pH drop, providing a new approach for solving a pH imbalance and improving hydrogen production. In-depth studies of the regulatory mechanism underlying ethanol-H₂ co-production metabolism and the syntrophic interactions of ethanol-H₂ co-producing Ethanoligenens with other microorganisms will provide insights into the improvement of bioenergy recovery in anaerobic biotechnology. The coupling of ETF with other biotechnologies, which based on the regulation of electron flow direction, syntrophic interaction, and metabolic flux, can be potential strategies to enhance the cascade recovery of energy and resources.

Rapid recruitment of hydrogen-producing biofilms for hydrogen production in a moving bed biofilm reactor by a sequential immobilization and deoxygenization approach

To reduce start-up time and enhance hydrogen production efficiency, a sequential immobilization and deoxygenization (SIDO) strategy for hydrogen production was investigated in continuous-flow moving bed biofilm reactors (MBBRs). The pre-immobilization process accelerated the initial enrichment of hydrogen-producing bacteria (HPB) and promoted the biofilm formation, which contribute to higher hydrogen production efficiency in SIDO-MBBRs compared to a non-immobilized reactor. A similar deoxygenization effect was achieved by inoculation with Pseudomonas aeruginosa compared with N₂ sparging, and the P. aeruginosa pre-immobilized MBBR (Pse-MBBR) showed a higher H₂ yield in the initial stage of operation. Microbial community analysis found a higher abundance of putative HPB in the range of 82.82-96.56%, with the predominant populations in the SIDO-MBBR assigned to genera Clostridium and Enterobacter. The results suggest that the SIDO-MBBR is an effective approach for rapid recruitment of HPB and start-up of fermentative hydrogen production.

Genome-centric microbiome analysis reveals solid retention time (SRT)-shaped species interactions and niche differentiation in food waste and sludge co-digesters

Co-digestion of food waste with sewage sludge is widely applied for waste stabilization and energy recovery around the world. However, the effect of solid retention time (SRT) on the microbial population dynamics, metabolism and interspecies interaction have not been fully elucidated. Here, the influence of SRTs (5-25 days) on the performance of the co-digestion system was investigated and state-of-the-art genome-centric metagenomic analysis was employed to uncover the dynamics and metabolic network of the key players underlying the well-functioned and poorly-functioned co-digestion microbial communities. The results of the microbial analyses indicated that SRT largely shaped microbial community structure by enriching the syntrophic specialist Syntrophomonas and CO₂/H₂ ( formate)-using methanogen Methanocorpusculum in the well-functioned co-digester operated at SRT of 25 days, while selecting acid-tolerant populations Lactobacillus at SRT of 5 days. The metagenome assembled genomes (MAGs) of key players, such as Syntrophomonadaceae, Methanocorpusculum, and Mesotoga, were retrieved, additionally, the syntrophic acetate oxidation plus hydrogenotrophic methanogenesis (SAO-HM) were proposed as the dominant pathway for methane production. The metabolic interaction in the co-digestion microbial consortia was profiled by assigning MAGs into functional guilds. Functional redundancy was found in the bacterial groups in hydrolysis step, and the members in these groups reduced the direct competition by niche differentiation.

Industrial wastewater to biohydrogen: Possibilities towards successful biorefinery route

The aim of this review is to summarize the modern developments and enhancement strategies reported for improving the biorefinery route of industrial wastewater to biohydrogen. Recent developments towards biohydrogen production chiefly involves culture enrichment, pretreatment of biocatalysts, co culture fermentation, metabolic and genetic engineering, ecobiotechnological approaches and the coupling process of biohydrogen. In addition, an overview of dark fermentation, pathways involved, microbes involved in biohydrogen production, industrial wastewater as substrate have been focused. The utilization of organic residuals of dark fermentation for subsequent value added products are highlighted. More apparently, the two stage coupling process and its possibilities towards biorefinery has been reviewed comprehensively. Moreover, comparative energy and economic aspects of biohydrogen production from industrial wastewater and its prospects towards pilot scale applications are also spotlighted. Though all the enhancement strategies have both benefits and disadvantages, coupling process is considered as the most successful biorefinery route for biohydrogen production.

Metabolic regulation of ethanol-type fermentation of anaerobic acidogenesis at different pH based on transcriptome analysis of Ethanoligenens harbinense

BACKGROUND

Ethanol-type fermentation, one of the fermentation types in mixed cultures of acidogenesis with obvious advantages such as low pH tolerance and high efficiency of H₂ production, has attracted widespread attentions. pH level greatly influences the establishment of the fermentation of carbohydrate acidogenesis by shaping community assembly and the metabolic activity of keystone populations. To explore the adaptation mechanisms of ethanol-type fermentation to low pH, we report the effects of initial pH on the physiological metabolism and transcriptomes of Ethanoligenens harbinense-a representative species of ethanol-type fermentation.

RESULTS

Different initial pH levels significantly changed the cell growth and fermentation products of E. harbinense. Using transcriptomic analysis, we identified and functionally categorized 1753 differentially expressed genes (DEGs). By mining information on metabolic pathways, we probed the transcriptional regulation of ethanol-H₂ metabolism relating to pH responses. Multiple pathways of E. harbinense were co-regulated by changing gene expression patterns. Low initial pH down-regulated the expression of cell growth- and acidogenesis-related genes but did not affect the expression of H₂ evolution-related hydrogenase and ferredoxin genes. High pH down-regulated the expression of H₂ evolution- and acidogenesis-related genes. Multiple resistance mechanisms, including chemotaxis, the phosphotransferase system (PTS), and the antioxidant system, were regulated at the transcriptional level under pH stress.

CONCLUSIONS

Ethanoligenens adapted to low pH by regulating the gene expression networks of cell growth, basic metabolism, chemotaxis and resistance but not H₂ evolution-related genes. Regulation based on pH shifts can represent an important approach to establish and enhance ethanol-type fermentation. The complete gene expression network of ethanol fermentative bacteria for pH response provides valuable insights into the acidogenic fermentation, and offers an effective regulation strategy for the sustainable energy recovery from wastewater and solid waste.

Regulating acidogenesis and methanogenesis for the separated bio-generation of hydrogen and methane from saline-to-hypersaline industrial wastewater

Given the limitations of acidogens and methanogens activities under saline environments, this work aims to optimize the main operational parameters affecting hydrogen and methane production from saline-to-hypersaline wastewater containing mono-ethylene glycol (MEG). MEG is the main contaminant in several saline industrial effluents. Anaerobic baffled reactor (ABR), as a multi-stage system, was used at different temperatures (i.e., 19-31 °C [ambient] and 35 °C), organic loading rates (OLRs) of 0.6-2.2 gCOD/L/d, and salinity of 5-35 gNaCl/L. Mesophilic conditions of 35 °C substantially promoted MEG biodegradability (92-98%) and hydrogen/methane productivity, even at elevated salinity. Hydrogen yield (HY) and methane yield (MY) peaked to 258 and 140 mL/gCOD_add, respectively, at OLR 0.64 gCOD/L/d and salinity up to 20-25 gNaCl/L. An immobilized sludge ABR (ISABR), packed with polyurethane media, was further compared with classical ABR, resulting in 1.8-fold higher MY, at 35 gNaCl/L. Microbial analysis showed that introducing attached growth system (ISABR) substantially promoted methanogens abundance, which was dominated by genus Methanosarcina. Among bacterial genera, Acetobacterium was dominant, particularly in 1^st compartment, representing MEG-degrading/salt-tolerant genus. At high salinity up to 35 gNaCl/L, the multi-phase and attached growth configuration can efficiently reduce the induced salt stress, particularly on methanogens, towards balanced and separated acidogenesis/methanogenesis. Overall, producing hydrogen and methane from anaerobic treatment of MEG-based saline wastewater is feasible at optimized parameters and configuration.

The complete genome sequence of Ethanoligenens harbinense reveals the metabolic pathway of acetate-ethanol fermentation: A novel understanding of the principles of anaerobic biotechnology

Ethanol-type fermentation is one of three main fermentation types in the acidogenesis of anaerobic treatment systems. Non-spore-forming Ethanoligenens is as a typical genus capable of ethanol-type fermentation in mixed culture (i.e. acetate-ethanol fermentation). This genus can produce ethanol, acetate, CO₂, and H₂ using carbohydrates, and has application potential in anaerobic bioprocesses. Here, the complete genome sequences and methylome of Ethanoligenens harbinense strains with different autoaggregative and coaggregative abilities were obtained using the PacBio single-molecule real-time sequencing platform. The genome size of E. harbinense strains was about 2.97-3.10 Mb with 55.5% G+C content. 3020-3153 genes were annotated, most of which were methylated at specific sites or motifs. The methylation types included 6mA, 4mC, and unknown types. Comparative genomic analysis demonstrated low levels of genetic similarity between E. harbinense and other well-known hydrogen-producing bacteria (i.e., Clostridium and Thermoanaerobacter) in phylogenesis. Hydrogen production of E. harbinense was catalyzed by genes that encode [FeFe]‑hydrogenases and that were synthesized by three maturases of [FeFe]-H₂ase. The metabolic mechanism of H₂-ethanol co-production fermentation, catalyzed by pyruvate ferredoxin oxidoreductase was proposed. This study provides genetic and evolutionary information of a model genus for the further investigation of the metabolic pathway and regulatory network of ethanol-type fermentation and anaerobic bioprocesses for waste or wastewater treatment.

Insights on acetate-ethanol fermentation by hydrogen-producing Ethanoligenens under acetic acid accumulation based on quantitative proteomics

Ethanoligenens, a novel ethanologenic hydrogen-producing genus, is a representative fermenter in its unique acetate-ethanol fermentation and physiology. Acetic acid accumulation is one of major factors that affect H₂-ethanol co-production. However, sufficient information is unavailable on the tolerance mechanisms of hydrogen-producing bacterium in acetic acid stress. The fermentation process of Ethanoligenens harbinense YUAN-3 was significantly slowed down in the selection stress of exogenous acetic acid. The maximum gas production rate of strain YUAN-3 decreased from 192.15 mL·(L-culture)^-1·h^-1 to 75.2 mL·(L-culture)^-1·h^-1 with increasing exogenous acetic acid from 0 mM to 30 mM, the batch fermentation period was correspondingly expanded from 66 h to 136 h. Through iTRAQ-based quantitative proteomic approach, 78, 121 and 216 proteins were differentially expressed after strain YUAN-3 was cultured in the medium supplemented with exogenous acetic acid of 10 mM, 20 mM and 30 mM. The up-regulated proteins were mainly involved in β-alanine and pyrimidine metabolism, oxidative stress response, while the down-regulated proteins mainly participated in phosphotransferase system (PTS), fructose and mannose metabolism, phosphate uptake, ribosome, and flagellar assembly. These proteins help to maintain balance between fermentation process and alleviation of intracellular acidification in strain YUAN-3. The study indicated that response to acetic acid stress in strain YUAN-3 was a complex process, which involved multiple metabolic pathways. Reductive pyrimidine catabolic pathway played an important role in the acetic acid resistance of E. harbinense.

Anaerobic degradation of sulfamethoxazole by mixed cultures from swine and sewage sludge

The objective of this study was to evaluate the anaerobic degradation of sulfamethoxazole (SMX) and the associated bacterial community changes in swine and sewage sludges. The degradation rate of SMX was higher in swine sludge than in sewage sludge. The addition of lactate, citrate, and sucrose had significant effects on SMX degradation, and sucrose addition yielded a higher SMX degradation rate than the other additives. At concentrations of 0.1-10 g/l sucrose, the SMX degradation rates increased in the sludge. The bacterial genera from swine sludge with sucrose exhibited the highest SMX degrading efficiency. Seventeen bacterial genera were found to be the major bacterial community members involved in SMX degradation in the sludge.

Quantitative proteomic analysis reveals the ethanologenic metabolism regulation of Ethanoligenens harbinense by exogenous ethanol addition

BACKGROUND

H₂-ethanol-coproducing bacteria, as primary fermenters, play important roles in the microbiome of bioreactors for bioenergy production from organic wastewater or solid wastes. Ethanoligenens harbinense YUAN-3 is an anaerobic ethanol-H₂-fermenting bacterium. Ethanol is one of the main end-products of strain YUAN-3 that influence its fermentative process. Until recently, the molecular mechanism of metabolic regulation in strain YUAN-3 during ethanol accumulation has still been unclear. This study aims to elucidate the metabolic regulation mechanisms in strain YUAN-3, which contributes to effectively shape the microbiome for biofuel and bioenergy production from waste stream.

RESULTS

This study reports that ethanol stress altered the distribution of end-product yields in the H₂-ethanol-coproducing Ethanoligenens harbinense strain YUAN-3. Decreasing trends of hydrogen yield from 1888.6 ± 45.8 to 837 ± 64.7 mL L^-1 and acetic acid yield from 1767.7 ± 45 to 160.6 ± 44.7 mg L^-1 were observed in strain YUAN-3 with increasing exogenous ethanol (0 mM-200 mM). However, the ethanol yield of strain YUAN-3 increased by 15.1%, 30.1%, and 27.4% in 50 mM, 100 mM, and 200 mM ethanol stress, respectively. The endogenous ethanol accounted for 96.1% (w/w) in liquid end-products when exogenous ethanol of 200 mM was added. The molar ratio of ethanol to acetic acid increased 14 times (exogenous ethanol of 200 mM) compared to the control. iTRAQ-based quantitative proteomic analysis indicated that 263 proteins of strain YUAN-3 were differentially expressed in 50 mM, 100 mM, and 200 mM of exogenous ethanol. These proteins are mainly involved in amino acid transport and metabolism, central carbon metabolism, and oxidative stress response.

CONCLUSION

These differentially expressed proteins play important roles in metabolic changes necessary for growth and survival of strain YUAN-3 during ethanol stress. The up-regulation of bifunctional acetaldehyde-CoA/alcohol dehydrogenase (ADHE) was the main reason why ethanol production was enhanced, while hydrogen gas and acetic acid yields declined in strain YUAN-3 during ethanol stress. This study also provides a new approach for the enhancement of ethanologenesis by H₂-ethanol-coproducing bacteria through exogenous ethanol addition.

Enhancement of corn stover conversion to carboxylates by extrusion and biotic triggers in solid-state fermentation

Solid-state fermentation is a potential technology for developing lignocellulosic biomass-based biorefineries. This work dealt with solid-state fermentation for carboxylates production from corn stover, as building blocks for a lignocellulosic feedstock-based biorefinery. The effect of extrusion pretreatment, together with the action of a microbial consortia and hydrolytic enzymes as biotic triggers, was investigated on corn stover conversion, microbial metabolic pathways, and populations. The extrusion caused changes in the physical and morphological characteristics, without altering the biochemical composition of the corn stover. Extrusion also led to remarkable differences in the composition of the indigenous microbial population of the substrate. Consequently, it affected the structure of community developed after fermentation and the substrate conversion yield, which increased by 118% (from 23 ± 4 gCOD/kgVSi obtained with raw substrate to 51 ± 1 gCOD/kgVSi with extruded corn stover) with regard to self-fermentation experiments. The use of activated sludge as inoculum further increased the total substrate conversion into carboxylates, up to 60 ± 2 gCOD/kgVSi, and shaped the microbial communities (mainly composed of bacteria from the Clostridia and Bacteroidia classes) with subsequent homogenization of the fermentation pathways. The addition of hydrolytic enzymes into the reactors further increased the corn stover conversion, leading to a maximum yield of 142 ± 1 gCOD/kgVSi. Thus, extrusion pretreatment combined with the use of an inoculum and enzyme addition increased by 506% corn stover conversion into carboxylates. Beside biomass pretreatment, the results of this study indicated that biotic factor greatly impacted solid-state fermentation by shaping the microbial communities and related metabolic pathways.

Inhibition of anaerobic digestion processes: Applications of molecular tools

Inhibition of anaerobic digestion (AD) due to perturbation caused by substrate composition and/or operating conditions can significantly reduce performance. Such perturbations could be limited by elucidating microbial community response to inhibitors and devising strategies to increase community resilience. To this end, advanced molecular methods are increasingly being applied to study the AD microbiome, a diverse community of microbial populations with complex interactions. This literature review of AD inhibition studies indicates that inhibitory concentrations are highly variable, likely stemming from differences in community structure or activity profile and previous exposure to inhibitors. More recent molecular methods such as 'omics' tools, substrate mapping, and real-time sequencing are helping to unravel the complexity of AD inhibition by elucidating physiological and ecological significance of key microbial populations. The AD community must strive towards developing predictive abilities to avoid system failure (e.g., real-time tracking of an indicator species) to improve resilience of AD systems.

Biohydrogen production at pH below 3.0: Is it possible?

Biological hydrogen production was investigated in continuous acidogenic reactors fed with sucrose at 30 °C without pH control. In the first experimental phase, three reactors were compared: a structured fixed-bed (FB), a granular UASB (UG) and a flocculent UASB (UF-1). They were run at 3.3 h HRT and 33 gCOD L^-1d^-1 OLR. Hydrogen production occurred throughout the experimental period with an average effluent pH of only 2.8. The FB, UG and UF-1 reactors presented volumetric hydrogen production rates (VHPR) of 95 ± 69, 45 ± 37 and 54 ± 32 mLH₂ L^-1h^-1, respectively; and H₂ yields (HY) of 1.5 ± 0.8, 0.8 ± 0.6 and 1.2 ± 0.7 molH₂ mol^-1 sucrose_consumed, respectively. The UF-1 reactor showed intermediate VHPR and HY, but no declining trend, contrary to what was observed in the FB reactor. Thus, aiming at continuous and long-term H₂ production, a flocculent UASB was applied in the second experimental phase. In this phase, the HRT of the acidogenic reactor, which was named UF-2, was raised to 4.6 h, resulting in an OLR of 25 gCOD L^-1d^-1. The VHPR and the HY increased considerably to 175 ± 44 mLH₂ L^-1h^-1 and 3.4 ± 0.7 molH₂ mol^-1 sucrose_consumed, respectively. These improvements were accompanied by greater sucrose removal, higher suspended biomass concentration, less production of lactate and more of acetate, and high ethanol concentration. Contradicting the current published literature data that reports strong inhibition of H₂ production by dark fermentation at pH less than 4.0, the UF-2 reactor presented stable, long-term H₂ production with satisfactory yields at pH 2.7 on average. 16 S rDNA sequencing revealed that two sequences assigned as Ethanoligenens and Clostridium accounted for over 70% of the microbiota in all the reactors. The non-necessity of adding alkalizing agents and the successful H₂ production under very acid conditions, demonstrated in this study, open a new field of investigation in biological hydrogen production by dark fermentation towards a more sustainable and feasible technology.

Assessing the colonic microbiome, hydrogenogenic and hydrogenotrophic genes, transit and breath methane in constipation

BACKGROUND

Differences in the gut microbiota and breath methane production have been observed in chronic constipation, but the relationship between colonic microbiota, transit, and breath tests remains unclear.

METHODS

In 25 healthy and 25 constipated females we evaluated the sigmoid colonic mucosal and fecal microbiota using 16S rRNA gene sequencing, abundance of hydrogenogenic FeFe (FeFe-hydA) and hydrogenotrophic (methyl coenzyme M reductase A [mrcA] and dissimilatory sulfite reductase A [dsrA]) genes with real-time qPCR assays, breath hydrogen and methane levels after oral lactulose, and colonic transit with scintigraphy.

KEY RESULTS

Breath hydrogen and methane were not correlated with constipation, slow colon transit, or with abundance of corresponding genes. After adjusting for colonic transit, the abundance of FeFehydA, dsrA, and mcrA were greater (P<.005) in colonic mucosa, but not stool, of constipated patients. The abundance of the selected functional gene targets also correlated with that of selected taxa. The colonic mucosal abundance of FeFe-hydA, but not mcrA, correlated positively (P<.05) with breath methane production, slow colonic transit, and overall microbiome composition. In the colonic mucosa and feces, the abundance of hydrogenogenic and hydrogenotrophic genes were positively correlated (P<.05). Breath methane production was not associated with constipation or colonic transit.

CONCLUSIONS & INFERENCES

Corroborating our earlier findings with 16S rRNA genes, colonic mucosal but not fecal hydrogenogenic and hydrogenotrophic genes were more abundant in constipated vs. healthy subjects independent of colonic transit. Breath gases do not directly reflect the abundance of target genes contributing to their production.

The pangenome of the genus Clostridium

The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.

Integrating microbial fuel cells with anaerobic acidification and forward osmosis membrane for enhancing bio-electricity and water recovery from low-strength wastewater

Microbial fuel cells (MFCs) and forward osmosis (FO) are two emerging technologies with great potential for energy-efficient wastewater treatment. In this study, anaerobic acidification and FO membrane were simultaneously integrated into an air-cathode MFC (AAFO-MFC) for enhancing bio-electricity and water recovery from low-strength wastewater. During a long-term operation of approximately 40 days, the AAFO-MFC system achieved a continuous and relatively stable power generation, and the maximum power density reached 4.38 W/m³. The higher bio-electricity production in the AAFO-MFC system was mainly due to the accumulation of ethanol resulted from anaerobic acidification process and the rejection of FO membrane. In addition, a proper salinity environment in the system controlled by the addition of MF membrane enhanced the electricity production. Furthermore, the AAFO-MFC system produced a high quality effluent, with the removal rates of organic matters and total phosphorus of more than 97%. However, the nitrogen removal was limited for the lower rejection of FO membrane. The combined biofouling and inorganic fouling were responsible for the lower water flux of FO membrane, and the Desulfuromonas sp. utilized the ethanol for bio-electricity production was observed in the anode. These results substantially improve the prospects for simultaneous wastewater treatment and energy recovery, and further studies are needed to optimize the system integration and operating parameters.

H2-Producing Bacterial Community during Rice Straw Decomposition in Paddy Field Soil: Estimation by an Analysis of [FeFe]-Hydrogenase Gene Transcripts

The transcription patterns of [FeFe]-hydrogenase genes (hydA), which encode the enzymes responsible for H2 production, were investigated during rice straw decomposition in paddy soil using molecular biological techniques. Paddy soil amended with and without rice straw was incubated under anoxic conditions. RNA was extracted from the soil, and three clone libraries of hydA were constructed using RNAs obtained from samples in the initial phase of rice straw decomposition (day 1 with rice straw), methanogenic phase of rice straw decomposition (day 14 with rice straw), and under a non-amended condition (day 14 without rice straw). hydA genes related to Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Thermotogae were mainly transcribed in paddy soil samples; however, their proportions markedly differed among the libraries. Deltaproteobacteria-related hydA genes were predominantly transcribed on day 1 with rice straw, while various types of hydA genes related to several phyla were transcribed on day 14 with rice straw. Although the diversity of transcribed hydA was significantly higher in the library on day 14 with rice straw than the other two libraries, the composition of hydA transcripts in the library was similar to that in the library on day 14 without rice straw. These results indicate that the composition of active H2 producers and/or H2 metabolic patterns dynamically change during rice straw decomposition in paddy soil.

Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia

High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.

Magnetite nanoparticles enable a rapid conversion of volatile fatty acids to methane

Evaluation of whether paddy soil enrichments obtained in the presence of magnetite and propionate can accelerate methane production from mixed volatile fatty acids.

Polarized potential and electrode materials implication on electro-fermentative di-hydrogen production: Microbial assemblages and hydrogenase gene copy variation

This study examined the changes in microbial diversity in response to different electrode materials viz., stainless steel mesh (SS) and graphite plate as anodes in two microbial electrolysis cell (MEC) each poised at 0.2V, 0.4V, 0.6V and 0.8V. Changes in microbiota prior to and after pretreatment along with microbiota enriched in response to various poised potentials with SS and graphite are monitored by 16S rRNA gene based DGGE profiling. Significant shifts in microbial community were noticed at all these experimental conditions. Correspondingly, the level of hydrogenase belonging to genera Bacillus, Pseudomonas, Rhodopseudomonas and Clostridium was studied by quantitative real time PCR (RT-PCR) at various applied potentials. DGGE based 16S rRNA gene profiling revealed enriched members belonging to phylum Firmicutes predominantly present at 0.8V in both MECs contributing to high hydrogen production. This study first time explored the growth behavior of mixed consortia in response to poised potentials and electrode materials.

Bromochloromethane, a Methane Analogue, Affects the Microbiota and Metabolic Profiles of the Rat Gastrointestinal Tract

Bromochloromethane (BCM), an inhibitor of methanogenesis, has been used in animal production. However, little is known about its impact on the intestinal microbiota and metabolic patterns. The present study aimed to investigate the effect of BCM on the colonic bacterial community and metabolism by establishing a Wistar rat model. Twenty male Wistar rats were randomly divided into two groups (control and treated with BCM) and raised for 6 weeks. Bacterial fermentation products in the cecum were determined, and colonic methanogens and sulfate-reducing bacteria (SRB) were quantified. The colonic microbiota was analyzed by pyrosequencing of the 16S rRNA genes, and metabolites were profiled by gas chromatography and mass spectrometry. The results showed that BCM did not affect body weight and feed intake, but it did significantly change the intestinal metabolic profiles. Cecal protein fermentation was enhanced by BCM, as methylamine, putrescine, phenylethylamine, tyramine, and skatole were significantly increased. Colonic fatty acid and carbohydrate concentrations were significantly decreased, indicating the perturbation of lipid and carbohydrate metabolism by BCM. BCM treatment decreased the abundance of methanogen populations, while SRB were increased in the colon. BCM did not affect the total colonic bacterial counts but significantly altered the bacterial community composition by decreasing the abundance of actinobacteria, acidobacteria, and proteobacteria. The results demonstrated that BCM treatment significantly altered the microbiotic and metabolite profiles in the intestines, which may provide further information on the use of BCM in animal production.

New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing

A fosmid metagenomic library was constructed with total community DNA obtained from a municipal wastewater treatment plant (MWWTP), with the aim of identifying new FeFe-hydrogenase genes encoding the enzymes most important for hydrogen metabolism. The dataset generated by pyrosequencing of a fosmid library was mined to identify environmental gene tags (EGTs) assigned to FeFe-hydrogenase. The majority of EGTs representing FeFe-hydrogenase genes were affiliated with the class Clostridia, suggesting that this group is the main hydrogen producer in the MWWTP analyzed. Based on assembled sequences, three FeFe-hydrogenase genes were predicted based on detection of the L2 motif (MPCxxKxxE) in the encoded gene product, confirming true FeFe-hydrogenase sequences. These sequences were used to design specific primers to detect fosmids encoding FeFe-hydrogenase genes predicted from the dataset. Three identified fosmids were completely sequenced. The cloned genomic fragments within these fosmids are closely related to members of the Spirochaetaceae, Bacteroidales and Firmicutes, and their FeFe-hydrogenase sequences are characterized by the structure type M3, which is common to clostridial enzymes. FeFe-hydrogenase sequences found in this study represent hitherto undetected sequences, indicating the high genetic diversity regarding these enzymes in MWWTP. Results suggest that MWWTP have to be considered as reservoirs for new FeFe-hydrogenase genes.

Clostridium perfringens septicemia in a long-beaked common dolphin Delphinus capensis: an etiology of gas bubble accumulation in cetaceans

An adult female long-beaked common dolphin Delphinus capensis live-stranded in La Jolla, California, USA, on July 30, 2012 and subsequently died on the beach. Computed tomography and magnetic resonance imaging revealed gas bubble accumulation in the vasculature, organ parenchyma, mandibular fat pads, and subdermal sheath as well as a gas-filled cavity within the liver, mild caudal abdominal effusion, and fluid in the uterus. Gross examination confirmed these findings and also identified mild ulcerations on the palate, ventral skin, and flukes, uterine necrosis, and multifocal parenchymal cavitations in the brain. Histological review demonstrated necrosis and round clear spaces interpreted as gas bubbles with associated bacterial rods within the brain, liver, spleen, and lymph nodes. Anaerobic cultures of the lung, spleen, liver, bone marrow, and abdominal fluid yielded Clostridium perfringens, which was further identified as type A via a multiplex PCR assay. The gas composition of sampled bubbles was typical of putrefaction gases, which is consistent with the by-products of C. perfringens, a gas-producing bacterium. Gas bubble formation in marine mammals due to barotrauma, and peri- or postmortem off-gassing of supersaturated tissues and blood has been previously described. This case study concluded that a systemic infection of C. perfringens likely resulted in production of gas and toxins, causing tissue necrosis.

Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil

Hydrogen (H2) is one of the most important intermediates in the anaerobic decomposition of organic matter. Although the microorganisms consuming H2 in anaerobic environments have been well documented, those producing H2 are not well known. In this study, we elucidated potential members of H2 -producing bacteria in a paddy field soil using clone library analysis of [FeFe]-hydrogenase genes. The [FeFe]-hydrogenase is an enzyme involved in H2 metabolism, especially in H2 production. A suitable primer set was selected based on the preliminary clone library analysis performed using three primer sets designed for the [FeFe]-hydrogenase genes. Soil collected in flooded and drained periods was used to examine the dominant [FeFe]-hydrogenase genes in the paddy soil bacteria. In total, 115 and 108 clones were analyzed from the flooded and drained paddy field soils, respectively. Homology and phylogenetic analysis of the clones showed the presence of diverse [FeFe]-hydrogenase genes mainly related to Firmicutes, Deltaproteobacteria, and Chloroflexi. Predominance of Deltaproteobacteria and Chloroflexi suggests that the distinct bacterial community possessed [FeFe]-hydrogenase genes in the paddy field soil. Our study revealed the potential members of H2 -producing bacteria in the paddy field soil based on their genetic diversity and the distinctiveness of the [FeFe]-hydrogenase genes.

Investigation of the FeFe-hydrogenase gene diversity combined with phylogenetic microbial community analysis of an anaerobic domestic sewage sludge

Biological hydrogen production through the anaerobic digestion is an environmental friendly alternative for satisfying future hydrogen demands. Microorganisms residing into waste water treatment plants are far from being exhaustively characterized and surveys on hydrogen production through FeFe-hydrogenase in such ecosystems are scarce. This study combined the analysis of 16S rRNA and [FeFe]-hydrogenase (hydA) genes with statistical tools to estimate richness and diversity of the microbial community of a domestic sewage treatment plant at the phylogenetic and functional levels. Archaeal groups were represented by 69 % of sequences assigned to Methanosarcinales and the remaining belonged to Methanomicrobiales. Within the bacterial library, 136 operational taxonomic units (OTUs) were distributed into 9 phyla, being 86 OTUs related to uncultivated bacteria. From these, 25 OTUs represented potential novel taxa within Synergistetes. Proteobacteria was the most predominant (36 % of the OTUs) and diversified phylogenetic group in the bacterial library, most of them assigned to the class Betaproteobacteria. Twenty-two putative hydA sequences were recovered into four distinct clusters and most of them were more closely related to each other than with sequences retrieved from databases, indicating they are hitherto undetected [Fe-Fe]-hydrogenase gene sequences. The richness estimates revealed that the number of sampled sequences was enough for full coverage of the archaeal diversity but not sufficient to cover both bacterial and hydA gene diversities. The results confirmed a great richness and diversity of bacterial and hydA sequences retrieved from the sewage sludge sample, suggesting such environment as a potential reservoir of new hydrogenase genes for biotechnological exploration.

Microbial community structure and dynamics in two-stage vs single-stage thermophilic anaerobic digestion of mixed swine slurry and market bio-waste

The microbial community of a thermophilic two-stage process was monitored during two-months operation and compared to a conventional single-stage process. Qualitative and quantitative microbial dynamics were analysed by Denaturing Gradient Gel Electrophoresis (DGGE) and real-time PCR techniques, respectively. The bacterial community was dominated by heat-shock resistant, spore-forming clostridia in the two-stage process, whereas a more diverse and dynamic community (Firmicutes, Bacteroidetes, Synergistes) was observed in the single-stage process. A significant evolution of bacterial community occurred over time in the acidogenic phase of the two-phase process with the selection of few dominant species associated to stable hydrogen production. The archaeal community, dominated by the acetoclastic Methanosarcinales in both methanogen reactors, showed a significant diversity change in the single-stage process after a period of adaptation to the feeding conditions, compared to a constant stability in the methanogenic reactor of the two-stage process. The more diverse and dynamic bacterial and archaeal community of single-stage process compared to the two-stage process accounted for the best degradation activity, and consequently the best performance, in this reactor. The microbiological perspective proved a useful tool for a better understanding and comparison of anaerobic digestion processes.

Hydrogen-producing microflora and Fe-Fe hydrogenase diversities in seaweed bed associated with marine hot springs of Kalianda, Indonesia

Microbial fermentation is a promising technology for hydrogen (H(2)) production. H(2) producers in marine geothermal environments are thermophilic and halotolerant. However, no one has surveyed an environment specifically for thermophilic bacteria that produce H(2) through Fe-Fe hydrogenases (H(2)ase). Using heterotrophic medium, several microflora from a seaweed bed associated with marine hot springs were enriched and analyzed for H(2) production. A H(2)-producing microflora was obtained from Sargassum sp., 16S rRNA genes and Fe-Fe H(2)ase diversities of this enrichment were also analyzed. Based on 16S rRNA genes analysis, 10 phylotypes were found in the H(2)-producing microflora showing 90.0-99.5 % identities to known species, and belonged to Clostridia, Gammaproteobacteria, and Bacillales. Clostridia were the most abundant group, and three Clostridia phylotypes were most related to known H(2) producers such as Anaerovorax odorimutans (94.0 % identity), Clostridium papyrosolvens (98.4 % identity), and Clostridium tepidiprofundi (93.1 % identity). For Fe-Fe H(2)ases, seven phylotypes were obtained, showing 63-97 % identities to known Fe-Fe H(2)ases, and fell into four distinct clusters. Phylotypes HW55-3 and HM55-1 belonged to thermophilic and salt-tolerant H(2)-producing Clostridia, Halothermothrix orenii-like Fe-Fe H(2)ases (80 % identity), and cellulolytic H(2)-producing Clostridia, C. papyrosolvens-like Fe-Fe H(2)ases (97 % identity), respectively. The results of both 16S rRNA genes and Fe-Fe H(2)ases surveys suggested that the thermophilic and halotolerant H(2)-producing microflora in seaweed bed of hot spring area represented previously unknown H(2) producers, and have potential application for H(2) production.

Convergent development of anodic bacterial communities in microbial fuel cells

Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m⁻²). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities

We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × -2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H(2)-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H(2) production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.

Application of molecular techniques on heterotrophic hydrogen production research

This paper reviews the application of molecular techniques in heterotrophic hydrogen production studies. Commonly used molecular techniques are introduced briefly first, including cloning-sequencing after polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP), fluorescence in situ hybridization (FISH) and quantitative real-time PCR. Application of the molecular techniques in heterotrophic hydrogen production studies are discussed in details, focusing on identification of new isolates for hydrogen production, characterization of microbial compositions in bioreactors, monitoring microbial diversity variation, visualization of microbial distribution in hydrogen-producing granular sludge, and quantification of various microbial populations. Some significant findings in recent hydrogen production studies with the application of molecular techniques are discussed, followed by a research outlook of the heterotrophic biohydrogen field.

Hydrogen production by the newly isolated Clostridium beijerinckii RZF-1108

A fermentative hydrogen-producing strain, RZF-1108, was isolated from a biohydrogen reactor, and identified as Clostridium beijerinckii on the basis of the 16S rRNA gene analysis and physiobiochemical characteristics. The effects of culture conditions on hydrogen production by C. beijerinckii RZF-1108 were investigated in batch cultures. The hydrogen production and growth of strain RZF-1108 were highly dependent on temperature, initial pH and substrate concentration. Yeast extract was a favorable nitrogen source for hydrogen production and growth of RZF-1108. Hydrogen production corresponded to cell biomass yield in different culture conditions. The maximum hydrogen evolution, yield and production rate of 2209ml H2/l medium, 1.97 mol H2/mol glucose and 104.20 ml H2/g CDWh(-1) were obtained at 9 g/l of glucose, initial pH of 7.0, inoculum volume of 8% and temperature of 35 °C, respectively. These results demonstrate that C. beijerinckii can efficiently produce H2, and is another model microorganism for biohydrogen investigations.

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism

Hydrogen (H₂) has an important role in the anaerobic degradation of organic carbon and is the basis for many syntrophic interactions that commonly occur in microbial communities. Little is known, however, with regard to the biotic and/or abiotic factors that control the distribution and phylogenetic diversity of organisms which produce H₂ in microbial communities. In this study, we examined the [FeFe]-hydrogenase gene (hydA) as a proxy for fermentative bacterial H₂ production along physical and chemical gradients in various geothermal springs in Yellowstone National Park (YNP), WY, USA. The distribution of hydA in YNP geothermal springs was constrained by pH to environments co-inhabited by oxygenic phototrophs and to environments predicted to have low inputs of abiotic H₂. The individual HydA asssemblages from YNP springs were more closely related when compared with randomly assembled communities, which suggests ecological filtering. Model selection approaches revealed that geographic distance was the best explanatory variable to predict the phylogenetic relatedness of HydA communities. This evinces the dispersal limitation imposed by the geothermal spring environment on HydA phylogenetic diversity even at small spatial scales. pH differences between sites is the second highest ranked explanatory variable of HydA phylogenetic relatedness, which suggests that the ecology related to pH imposes strong phylogenetic niche conservatism. Collectively, these results indicate that pH has imposed strong niche conservatism on fermentative bacteria and that, within a narrow pH realm, YNP springs are dispersal limited with respect to fermentative bacterial communities.

Succession of the bacterial community and dynamics of hydrogen producers in a hydrogen-producing bioreactor

Variation in the hydrogen production rate was consistent with the succession of dominant bacteria during the batch fermentation process. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes and quantitative analysis of the hydA genes at both the DNA and mRNA levels confirmed that Clostridium perfringens was the most dominant hydrogen producer in the bioreactor.

Detection and quantification of functional genes of cellulose- degrading, fermentative, and sulfate-reducing bacteria and methanogenic archaea

Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide primers were designed and validated to amplify both sequenced and unsequenced glycoside hydrolase genes of cellulose-degrading bacteria, hydA genes of fermentative bacteria, dsrA genes of sulfate-reducing bacteria, and mcrA genes of methanogenic archaea. Specificity was verified in silico and by cloning and sequencing of PCR products obtained from an environmental sample characterized by the target functions. The primer pairs were further adapted to quantitative PCR (Q-PCR), and the method was demonstrated on samples obtained from two sulfate-reducing bioreactors treating mine drainage, one lignocellulose based and the other ethanol fed. As expected, the Q-PCR analysis revealed that the lignocellulose-based bioreactor contained higher numbers of cellulose degraders, fermenters, and methanogens, while the ethanol-fed bioreactor was enriched in sulfate reducers. The suite of primers developed represents a significant advance over prior work, which, for the most part, has targeted only pure cultures or has suffered from low specificity. Furthermore, ensuring the suitability of the primers for Q-PCR provided broad quantitative access to genes that drive critical anaerobic catalytic processes.

Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobes and anoxic enrichments from a moderately acidic fen

Newly designed primers for [Fe-Fe]-hydrogenases indicated that (i) fermenters, acetogens, and undefined species in a fen harbor hitherto unknown hydrogenases and (ii) Clostridium- and Thermosinus-related primary fermenters, as well as secondary fermenters related to sulfate or iron reducers might be responsible for hydrogen production in the fen. Comparative analysis of [Fe-Fe]-hydrogenase and 16S rRNA gene-based phylogenies indicated the presence of homologous multiple hydrogenases per organism and inconsistencies between 16S rRNA gene- and [Fe-Fe]-hydrogenase-based phylogenies, necessitating appropriate qualification of [Fe-Fe]-hydrogenase gene data for diversity analyses.

Microbial community structure in an integrated A/O reactor treating diluted livestock wastewater during start-up period

In order to investigate the correlation between reactor performance and the microorganisms, an integrated NO reactor was operated for 72 days to treat diluted livestock wastewater. Chemical oxygen demand (COD) removal efficiency increased from 79% to 94%, with total nitrogen (TN) removal efficiency from 37% to 50% (HRT 7.4 br) when the influent COD and TN were ca. 1500 mg/L and 95 mg/L, respectively, and the outlet COD concentration was less than 100 mg/L at the end. Microbial community was monitored during start-up period by denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA gene. DGGE profiles showed that microbial community had changed significantly during the start-up and these shifts were in accordance with the reactor performance. UPGMA clustering analysis showed that 14 anaerobic samples fell into five main groups and so did the aerobic ones, but the grouping patterns were different. Phylogenetic analysis indicated that microbial populations in the anaerobic compartment belonged to Firmicutes, Proteobacteria, Chioroflexi and Bacteroidetes, while Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobiae and Nitrospira were present in the aerobic compartment. In the anaerobic compartment, more fermentative and acetogenic bacteria were detected during the start-up while denitrifying bacteria faded away. Two functional populations such as Nitrospira defluvii and Dechioromonas denitnficans were observed when nitrogen removal was high, indicating that simultaneous nitrification and denitrification occurred in the aerobic compartment.