Physiological and phylogenetic characterization of a stable benzene-degrading, chlorate-reducing microbial community

Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments

Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g. through water radiolysis, or biotically, e.g. through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters, that strictly aerobic microorganisms are present in many apparently anoxic habitats, and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla, most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in situ production in up to half of the studied environments. Geochemical and microbiological data support the conclusion that "dark oxygen production" is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Indoor air VOCs biofiltration by bioactive coating packed bed bioreactors

Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low concentrations, the wide range of compounds and the hydrophobicity of some indoor air VOCs, which are the most important bottlenecks regarding the implementation of conventional biotechnologies for indoor air treatment. A bioactive coating-based bioreactor was tested in this study for the abatement of different VOCs (n-hexane, toluene and α-pinene) at different empty bed residence times (EBRT) and inlet VOC concentrations. The performance of this reactor was compared with a conventional biofilm-based bioreactor operated with the same microbial inoculum. After an acclimation period, the bioactive coating-based bioreactor achieved abatements of over 50% for hexane, 80% for toluene and 70% for pinene at EBRTs of 112-56 s and inlet concentrations of 9-15 mg m-3. These results were about 25, 10 and 20% lower than the highest removals recorded in the biofilm-based bioreactor. Both bioreactors experienced a decrease in VOC abatement by ∼25% for hexane, 45% for toluene and 40% for pinene, after reducing the EBRT to 28 s. When inlet VOC concentrations were progressively reduced, VOC abatement efficiencies did not improve. This fact suggested that low EBRTs and low inlet VOCs concentration hindered indoor air pollutant abatement as a result of a limited mass transfer and bioavailability. Metagenomic analyses showed that process operation with toluene, hexane and pinene as the only carbon and energy sources favored an enriched bacterial community represented by the genera Devosia, Mesorhizobium, Sphingobacterium and Mycobacterium, regardless of the bioreactor configuration. Bioactive coatings were used in this work as packing material of a conventional bioreactor, achieving satisfactory VOC abatement similar to a conventional bioreactor.

Boosting o-xylene removal and power generation in an airlift microbial fuel cell system

Microbial fuel cells (MFCs) are widely acknowledged to be a promising eco-friendly abatement technology of pollutants, and are capable of generating electricity. However, the poor mass transfer and reaction rate in MFCs significantly decrease their treatment capacity for contaminants, especially hydrophobic substances. The present work developed a novel MFC integrated with an airlift (ALR) reactor using a polypyrrole modified anode to promote the bioaccessibility of gaseous o-xylene and attachment of microorganisms. The results indicated that the established ALR-MFC system showed excellent elimination capability, with removal efficiency exceeding 84% even at high o-xylene concentration (1600 mg m^-3). The maximum output voltage of 0.549 V and power density of 13.16 mW m^-2 obtained by the Monod-type model were approximately twice and sixfold higher than that of a conventional MFC, respectively. According to the microbial community analysis, the superior performances of the ALR-MFC in terms of o-xylene removal and power generation were mainly ascribed to the enrichment of degrader (i.e. Shinella) and electrochemical active bacteria (i.e. Proteiniphilum). Moreover, the electricity generation of the ALR-MFC did not decrease at a high O₂ concentration, as O₂ was conducive to o-xylene degradation and electron release. The supplication of an external carbon source such as sodium acetate (NaAc) was conducive to increasing output voltage and coulombic efficiency. The electrochemical analysis revealed that released electrons can be transmitted with the action of NADH dehydrogenase to OmcZ, OmcS, and OmcA outer membrane proteins via a direct or indirect pathway, and ended up transferring to the anode directly.

Insights into the syntrophic microbial electrochemical oxidation of toluene: a combined chemical, electrochemical, taxonomical, functional gene-based, and metaproteomic approach

Biodegradation of aromatic hydrocarbons in anoxic contaminated environments is typically limited by the lack of bioavailable electron acceptors. Microbial electrochemical technologies (METs) are able to provide a virtually inexhaustible electron acceptor in the form of a solid electrode. Recently, we provided first experimental evidence for the syntrophic degradation of toluene in a continuous-flow bioelectrochemical reactor known as the "bioelectric well". Herein, we further analyzed the structure and function of the electroactive toluene-degrading microbiome using a suite of chemical, electrochemical, phylogenetic, proteomic, and functional gene-based analyses. The bioelectric well removed 83 ± 7 % of the toluene from the influent with a coulombic efficiency of 84 %. Cyclic voltammetry allowed to identify the formal potentials of four putative electron transfer sites, which ranged from -0.2 V to +0.1 V vs. SHE, consistent with outer membrane c-type cytochromes and pili of electroactive Geobacter species. The biofilm colonizing the surface of the anode was indeed highly enriched in Geobacter species. On the other hand, the planktonic communities thriving in the bulk of the reactor harbored aromatic hydrocarbons degraders and fermentative propionate-producing microorganisms, as revealed by phylogenetic and proteomic analyses. Most likely, propionate, acetate or other VFAs produced in the bulk liquid from the degradation of toluene were utilized as substrates by the electroactive biofilm. Interestingly, key-functional genes related to the degradation of toluene were found both in the biofilm and in the planktonic communities. Taken as a whole, the herein reported results highlight the importance of applying a comprehensive suite of techniques to unravel the complex cooperative metabolisms occurring in METs.

Effects of substrate fluctuation on the performance, microbial community and metabolic function of a biofilter for gaseous dichloromethane treatment

Dichloromethane (DCM) is a harmful volatile organic compound that usually originates from pharmaceutical industry. In this study, the treatment of gaseous DCM in a biofilter was investigated by gradually increasing the DCM inlet concentration. Nearly 80% of DCM could be removed when the inlet concentration was lower than 0.30 g m^-3. The maximum elimination capacity of 26.6 g m^-3·h^-1 was achieved at an inlet loading rate of 38.4 g m^-3·h^-1. However, with the increase in the inlet concentration to more than 0.60 g m^-3, the removal efficiency obviously decreased to about 40%. After a starvation period of 2 weeks, the biofilter rapidly recovered its performance. The Haldane model including a substrate inhibition term was applied to describe the kinetics of the biofilter. High-throughput sequencing indicated that DCM-degrading genera, such as Rhodanobacter sp., Hyphomicrobium sp., Rhizomicrobium sp., Bacillus sp., Pseudomonas sp., and Clostridium sp., were dominant in the biofilter in different operation phases. The microbial communities and diversities were greatly affected by the DCM concentration. Microbial metabolic functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results indicated that xenobiotics biodegradation and metabolism, carbohydrate metabolism, and amino acid metabolism were the three most abundant metabolic pathways of the microbes. The abundances of these metabolic functions were also altered by the DCM concentration.

Bioturbation effect of fortified Daqu on microbial community and flavor metabolite in Chinese strong-flavor liquor brewing microecosystem

Traditional spontaneous fermentation in microecosystem with microbial successions and environmental variables results in inconsistent quality of fermented foods. We therefore propose the directional bioturbation for microbiota regulation and metabolites production in food fermentation. Here, we revealed the bioturbation effect of fortified Daqu on microbial community based on taxonomic composition, co-occurrence network, and metabolic potential, using Chinese strong-flavor liquor fermentation as a microecosystem. According to principal coordinate analysis, microbial communities were obviously influenced by the bioturbation of fortified Daqu. More specifically, bioturbation increased the abundances of Caproiciproducens, Clostridium, Aspergillus, Candida, Methanobacterium, and Methanosarcina, while decreased that of Lactobacillus. Meanwhile, higher abundances of most genes that encoding enzymes involved in interspecies hydrogen transfer between hexanoic acid bacteria and methanogens were observed in the bioturbated ecosystem by PICRUSt approach. Additionally, co-occurrence analysis showed that bioturbation increased the diversity and complexity of interspecies interactions in microecosystem, which contributed to higher production of flavor metabolites such as hexanoic acid, ethyl hexanoate, and hexyl hexanoate. These results indicated that the bioturbation of fortified Daqu is feasible for flavor metabolism by interspecies interactions of functional microbiota in liquor fermentation. Taken together, it is of great importance for regulating Chinese liquor and even other foods fermentation by bioturbation.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

Ethanol content in different gasohol blend spills influences the decision-making on remediation technologies

Gasohol blend spills with variable ethanol content exert different electron acceptor demands in groundwater and the distinct dynamics undergone by these blends underscores the need for field-based information to aid decision-making on suitable remediation technologies for each gasohol blend spill. In this study, a comparison of two gasohol releases (E10 (10:90 ethanol and gasoline, v/v) and E25 (25:75 ethanol and gasoline, v/v) under monitored natural attenuation (MNA) and nitrate biostimulation, respectively) was conducted to assess the most effective remediation strategy for each gasohol release. Microbial communities were assessed to support geochemical data as well as to enable the characterization of important population shifts that evolve during biodegradation processes in E25 and E10 field experiments. Results revealed that natural attenuation processes sufficiently supported ethanol and BTEX compounds biodegradation in E10 release, due to the lower biochemical oxygen demand they exert relative to E25 blend. In E25 release, nitrate reduction was largely responsible for BTEX and ethanol biodegradation, as intended. First-order decay constants demonstrated that ethanol degradation rates were similar (p < 0.05) for both remediation technologies (2.05 ± 0.15 and 2.22 ± 0.23, for E25 and E10, respectively) whilst BTEX compounds exhibited different degradation rates (p > 0.05) that were higher for the experiment under MNA (0.33 ± 0.06 and 0.43 ± 0.03, for E25 and E10, respectively). Therefore, ethanol content in different gasohol blends can influence the decision-making on the most suitable remediation technology, as MNA processes can be applied for the remediation of gasohol blends with lower ethanol content (i.e., 10% v/v), once the aquifer geochemical conditions provide a sufficient electron acceptor pool. To the best of our knowledge, this is the first field study to monitor two long-term gasohol releases over various time scales in order to assess feasible remediation technologies for each scenario.

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.

Enhanced degradation of phenolic compounds in coal gasification wastewater by a novel integration of micro-electrolysis with biological reactor (MEBR) under the micro-oxygen condition

The aim of this work was to study an integration of micro-electrolysis with biological reactor (MEBR) for strengthening removal of phenolic compounds in coal gasification wastewater (CGW). The results indicated MEBR achieved high efficiencies in removal of COD and phenolic compounds as well as improvement of biodegradability of CGW under the micro-oxygen condition. The integrated MEBR process was more favorable to improvement of the structural stability of activated sludge and biodiversity of specific functional microbial communities. Especially, Shewanella and Pseudomonas were enriched to accelerate the extracellular electron transfer, finally facilitating the degradation of phenolic compounds. Moreover, MEBR process effectively relieved passivation of Fe-C filler surface and prolonged lifespan of Fe-C filler. Accordingly, the synergetic effect between iron-carbon micro-electrolysis (ICME) and biological action played a significant role in performance of the integrated process. Therefore, the integrated MEBR was a promising practical process for enhancing CGW treatment.

Comparison of bacterial community characteristics between complete and shortcut denitrification systems for quinoline degradation

For quinoline-denitrifying degradation, very few researches focused on shortcut denitrification process and its bacterial community characteristics. In this study, complete and shortcut denitrification systems were constructed simultaneously for quinoline degradation. By calculation, specific quinoline removal rates were 0.905 and 1.123 g/(gVSS d), respectively, in the complete and shortcut systems, and the latter was 1.24 times of the former. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), high-throughput sequencing, and quantitative PCR (qPCR) techniques based on 16S rRNA were jointly applied to compare microbial community structures of two systems. Many denitrifying bacteria phyla, classes, and genera were detected in the two systems. Phylum Proteobacteria, Class Gammaproteobacteria, and Genus Alicycliphilus denitrificans were the dominant contributors for quinoline-denitrifying degradation. In the shortcut denitrification system, main and specific strains playing crucial roles were more; the species richness and the total abundance of functional genes (narG, nirS, nirK, and nosZ) were higher compared with the complete denitrification system. It could be supposed that inorganic-nitrogen reductase activity of bacterial community was stronger in the shortcut denitrification system, which was the intrinsic reason to result in higher denitrification rate.

Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica

Microbial pinnacles in ice-covered Lake Vanda, McMurdo Dry Valleys, Antarctica, extend from the base of the ice to more than 50 m water depth. The distribution of microbial communities, their photosynthetic potential, and pinnacle morphology affects the local accumulation of biomass, which in turn shapes pinnacle morphology. This feedback, plus environmental stability, promotes the growth of elaborate microbial structures. In Lake Vanda, all mats sampled from greater than 10 m water depth contained pinnacles with a gradation in size from <1-mm-tall tufts to pinnacles that were centimeters tall. Small pinnacles were cuspate, whereas larger ones had variable morphology. The largest pinnacles were up to ~30 cm tall and had cylindrical bases and cuspate tops. Pinnacle biomass was dominated by cyanobacteria from the morphological and genomic groups Leptolyngbya, Phormidium, and Tychonema. The photosynthetic potential of these cyanobacterial communities was high to depths of several millimeters into the mat based on PAM fluorometry, and sufficient light for photosynthesis penetrated ~5 mm into pinnacles. The distribution of photosynthetic potential and its correlation to pinnacle morphology suggests a working model for pinnacle growth. First, small tufts initiate from random irregularities in prostrate mat. Some tufts grow into pinnacles over the course of ~3 years. As pinnacles increase in size and age, their interiors become colonized by a more diverse community of cyanobacteria with high photosynthetic potential. Biomass accumulation within this subsurface community causes pinnacles to swell, expanding laminae thickness and creating distinctive cylindrical bases and cuspate tops. This change in shape suggests that pinnacle morphology emerges from a specific distribution of biomass accumulation that depends on multiple microbial communities fixing carbon in different parts of pinnacles. Similarly, complex patterns of biomass accumulation may be reflected in the morphology of elaborate ancient stromatolites.

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC

Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor.

Methane oxidation linked to chlorite dismutation

We examined the potential for CH₄ oxidation to be coupled with oxygen derived from the dissimilatory reduction of perchlorate, chlorate, or via chlorite (ClO⁻₂) dismutation. Although dissimilatory reduction of ClO⁻₄ and ClO⁻₃ could be inferred from the accumulation of chloride ions either in spent media or in soil slurries prepared from exposed freshwater lake sediment, neither of these oxyanions evoked methane oxidation when added to either anaerobic mixed cultures or soil enriched in methanotrophs. In contrast, ClO⁻₂ amendment elicited such activity. Methane (0.2 kPa) was completely removed within several days from the headspace of cell suspensions of Dechloromonas agitata CKB incubated with either Methylococcus capsulatus Bath or Methylomicrobium album BG8 in the presence of 5 mM ClO⁻₂. We also observed complete removal of 0.2 kPa CH₄ in bottles containing soil enriched in methanotrophs when co-incubated with D. agitata CKB and 10 mM ClO⁻₂. However, to be effective these experiments required physical separation of soil from D. agitata CKB to allow for the partitioning of O₂ liberated from chlorite dismutation into the shared headspace. Although a link between ClO⁻₂ and CH₄ consumption was established in soils and cultures, no upstream connection with either ClO⁻₄ or ClO⁻₃ was discerned. This result suggests that the release of O₂ during enzymatic perchlorate reduction was negligible, and that the oxygen produced was unavailable to the aerobic methanotrophs.

Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation

Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. Alicycliphilus denitrificans strain BC can use chlorate, nitrate, and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis, and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells are shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. All MS data have been deposited in the ProteomeXchange with identifier PXD000258.

An open source chimera checker for the fungal ITS region

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at http://www.emerencia.org/chimerachecker.html) to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.)

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601^T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601^T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601^T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601^T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601^T. Genes involved in cyclohexanol degradation were only found in strain K601^T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.

The combined effect of decabromodiphenyl ether (BDE-209) and copper (Cu) on soil enzyme activities and microbial community structure

Waste electrical and electronic equipment (e-waste) is now the fastest growing waste stream in the world. It is reported that polybrominated diphenyl ethers (PBDEs) and heavy metals were main contaminants in e-waste recycling site. Among these contaminants BDE-209 and Cu were widespread, yet their combined effect on soil enzyme activities and microbial community structure are not well understood. In this study, the ecotoxicological effects of both combined and single pollution of BDE-209 and Cu at different concentration levels were studied under laboratory conditions. The activities of soil catalase, urease and saccharase were sensitive to BDE-209 and Cu pollution. Although the enzyme activities varied over time, the concentration effects were obvious. Statistical analyses revealed that, at the same incubation time, as the concentration of BDE-209 or Cu increased, the enzyme activities were decreased. Combined effects of both BDE-209 and Cu were different from that of BDE-209 or Cu alone. Enzyme activities data were essentially based on the multiple regression technique. The results showed that the action and interaction between BDE-209 and Cu were strongly dependent on the exposure time, as the combined effects of BDE-209 and Cu were either synergistic or antagonistic at different incubation times. Soil catalase and saccharase were more comfortable used as indicators of BDE-209 and Cu combined pollution, as the variation trends were similar to the single contaminant treatments, and the responses were quick and significant. Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA gene showed that BDE-209 and Cu pollution altered the bacterial community structure by promoting changes in species composition and species richness. The existence of BDE-209 and Cu in soils reduced the microbial diversity, and the concentration effects were obvious. Overall, microbial diversity in the combined treatments were lower than the single ones, and when the concentration of BDE-209 and Cu increased, and the Shannon-Weaver index decreased, which indicated the combined effect of BDE-209 and Cu on the microbial community structure was synergistic. Our results further the understanding of the toxic effects of BDE-209 and Cu on soil enzyme activities and microbial community structure, and suggest the need for more in-depth analysis to increase progressively the understanding of the toxicological mechanisms involved.

Performance and microbial community in hybrid Anaerobic Baffled Reactor-constructed wetland for nitrobenzene wastewater

A process combining an Anaerobic Baffled Reactor (ABR) and a constructed wetland was employed to treat nitrobenzene wastewater. The overall performance was examined throughout long-term operation with a hydraulic retention time (HRT) of 24 h at 30±1 °C. The effluent nitrobenzene concentration of the ABR and constructed wetland was less than 4.81 and 1.94 mg/L, respectively, with an initial nitrobenzene concentration of 80 mg/L at the steady-state periods. The corresponding removal efficiencies were 97.02% and 73.93%, respectively. Moreover, 97.29% of aniline produced in the ABR could be removed in the subsequent wetland. The number of sequenced clones from each library was sufficient to cover archaea and eubacteria diversity at the species level and to obtain a representation of the total microbial diversity in the ABR. The predominant microbial populations in the ABR were identified as Pseudomonas putida, Methanosaeta concilii and Methanothrix soehngenii.

Transformation of microflora during degradation of gaseous toluene in a biofilter detected using PCR-DGGE

A laboratory-scale biofiltration system, the rotatory-switching biofilter (RSB), was operated for 199 days using toluene as a model pollutant. The target gaseous pollutant for the biofiltration experiment was approximately 300 ppmv of toluene. Toluene removal efficiency (RE, %) was initially approximately 20% with a 247-ppmv concentration (0.9 g m(-3)) of toluene during the first 10 days. Although the RE decreased several times whenever nitrogen was consumed, it again reached almost 100% when the nitrogen source was in sufficient supply. Denaturing gradient gel electrophoresis (DGGE) analysis was employed to assess the transformation ofmicroflora during operation of the biofilter The results based on a 16S rRNA gene profile showed that the microbial community structure changed with operation time. Although the microflora changed during the initial period (before day 40), transformation of the bacterial component was hardly observed after day 51. Statistical analyses of the DGGE profiles indicated that the bacterial community was almost unaffected by the environmental factors, such as adding ozone, high-level nitrogen supply, increase of loading toluene, and the shutdown of the RSB. The DGGE profile using tmoA-like genes, which encode proteins belonging to the hydroxylase component mono-oxygenases involved in the initial attack of aerobic benzene, toluene, ethylbenzene, and xylene degradation, confirmed the existence of toluene-degrading bacteria. There were at least four kinds of toluene-degradable bacteria having tmoA-like genes up to day 36, which decreased to two species after day 40. Sequence analysis after DGGE profiling revealed that Burkholderia cepacia, Sphingobacterium multivorum, and Pseudomonas putida were present in the biofilter. Only Alicycliphilus denitrificans was present throughout the whole operation period. In the initial stage of operating the RSB, many types of bacteria may have tried to adapt to the conditions, and subsequently, only selected bacteria were able to grow and to degrade toluene.

Anaerobic benzene degradation under denitrifying conditions: Peptococcaceae as dominant benzene degraders and evidence for a syntrophic process

An anaerobic microbial community was enriched in a chemostat that was operated for more than 8 years with benzene and nitrate as electron acceptor. The coexistence of multiple species in the chemostat and the presence of a biofilm, led to the hypothesis that benzene-degrading species coexist in a syntrophic interaction, and that benzene can be degraded in syntrophy by consortia with various electron acceptors in the same culture. The benzene-degrading microorganisms were identified by DNA-stable isotope probing with [U-(13) C]-labelled benzene, and the effect of different electron donors and acceptors on benzene degradation was investigated. The degradation rate constant of benzene with nitrate (0.7 day(-1) ) was higher than reported previously. In the absence of nitrate, the microbial community was able to use sulfate, chlorate or ferric iron as electron acceptor. Bacteria belonging to the Peptococcaceae were identified as dominant benzene consumers, but also those related to Rhodocyclaceae and Burkholderiaceae were found to be associated with the anaerobic benzene degradation process. The benzene degradation activity in the chemostat was associated with microbial growth in biofilms. This, together with the inhibiting effect of hydrogen and the ability to degrade benzene with different electron acceptors, suggests that benzene was degraded via a syntrophic process.

Assimilation of benzene carbon through multiple trophic levels traced by different stable isotope probing methodologies

The flow of benzene carbon along a food chain consisting of bacteria and eukaryotes, including larvae (Diptera: Chironomidae), was evaluated by total lipid fatty acids (TLFAs)-, amino acid- and protein-stable isotope probing (SIP). A coconut-fibre textile, colonized by a benzene-degrading biofilm, was sampled in a system established for the remediation of benzene, toluene, ethylbenzene and xylenes (BTEX)-polluted groundwater and incubated with (12)C- and [(13)C(6)]-benzene (>99 at.%) in a batch-scale experiment for 2-8 days. After 8 days, Chironomus sp. larvae were added to study carbon flow to higher trophic levels. Gas chromatography-combustion-isotope ratio monitoring mass spectrometry of TLFA showed increased isotope ratios in the (13)C-benzene-incubated biofilm. A higher (13)C-enrichment was observed in TLFAs, indicative of Gram-negative bacteria than for Gram-positive. Fatty acid indicators of eukaryotes showed significant (13)C-incorporation, but to a lower extent than bacterial indicators. Fatty acids extracted from larvae feeding on (13)C-biofilm reached an isotopic ratio of 1.55 at.%, illustrating that the larvae feed, to some extent, on labelled biomass. No (13)C-incorporation was detectable in larval proteins after their separation by sodium-dodecyl sulphate-polyacrylamide gel electrophoresis and analysis by nano-liquid-chromatography-mass spectrometry. The flow of benzene-derived carbon could be traced in a food web consisting of bacteria and eukaryotes.

Long term performance of an arsenite-oxidizing-chlorate-reducing microbial consortium in an upflow anaerobic sludge bed (UASB) bioreactor

A chlorate (ClO(3)(-)) reducing microbial consortium oxidized arsenite (As(III)) to arsenate (As(V)) in an upflow anaerobic sludge-bed bioreactor over 550 days operation. As(III) was converted with high conversion efficiencies (>98%) at volumetric loadings ranging from 0.45 to 1.92 mmol As/(L(reactor)d). The oxidation of As(III) was linked to the complete reduction of ClO(3)(-) to Cl(-) and H(2)O, as demonstrated by a molar ratio of approximately 3.0 mol As(III) oxidized per mole of Cl(-) formed and by the greatly lowered ClO(3)(-)-reducing capacity without As(III) feeding. An autotrophic enrichment culture was established from the bioreactor biofilm. A 16S rRNA gene clone library indicated that the culture was dominated by Dechloromonas, and Stenotrophomonas as well as genera within the family Comamonadaceae. The results indicate that the oxidation of As(III) to less mobile As(V) utilizing ClO(3)(-) as a terminal electron acceptor provides a sustainable bioremediation strategy for arsenic contamination in anaerobic environments.

Anaerobic benzene degradation by bacteria

Benzene is a widespread and toxic contaminant. The fate of benzene in contaminated aquifers seems to be primarily controlled by the abundance of oxygen: benzene is aerobically degraded at high rates by ubiquitous microorganisms, and the oxygen‐dependent pathways for its breakdown were elucidated more than 50 years ago. In contrast, benzene was thought to be persistent under anoxic conditions until 25 years ago. Nevertheless, within the last 15 years, several benzene‐degrading cultures have been enriched under varying electron acceptor conditions in laboratories around the world, and organisms involved in anaerobic benzene degradation have been identified, indicating that anaerobic benzene degradation is a relevant environmental process. However, only a few benzene degraders have been isolated in pure culture so far, and they all use nitrate as an electron acceptor. In some highly enriched strictly anaerobic cultures, benzene has been described to be mineralized cooperatively by two or more different organisms. Despite great efforts, the biochemical mechanism by which the aromatic ring of benzene is activated in the absence of oxygen is still not fully elucidated; methylation, hydroxylation and carboxylation are discussed as likely reactions. This review summarizes the current knowledge about the ‘key players’ of anaerobic benzene degradation under different electron acceptor conditions and the possible pathway(s) of anaerobic benzene degradation.

Anaerobic degradation of non-substituted aromatic hydrocarbons

Aromatic hydrocarbons are among the most prevalent organic pollutants in the environment. Their removal from contaminated systems is of great concern because of the high toxicity effect on living organisms including humans. Aerobic degradation of aromatic hydrocarbons has been intensively studied and is well understood. However, many aromatics end up in habitats devoid of molecular oxygen. Nevertheless, anaerobic degradation using alternative electron acceptors is much less investigated. Here, we review the recent literature and very early progress in the elucidation of anaerobic degradation of non-substituted monocyclic (i.e. benzene) and polycyclic aromatic hydrocarbons (PAH such as naphthalene and phenanthrene). A focus will be on benzene and naphthalene as model compounds. This review concerns the microbes involved, the biochemistry of the initial activation and subsequent enzyme reactions involved in the pathway.

Anaerobic benzene biodegradation by a pure bacterial culture of Bacillus cereus under nitrate reducing conditions

A pure culture using benzene as sole carbon and energy sources was isolated by screening procedure from gasoline contaminated soil. The analysis of the 16S rDNA gene sequence, morpholpgical and physiological characteristics showed that the isolated strain was a member of genus Bacillus cereus. The biodegradation performance of benzene by B. cereus was evaluated, and the results showed that benzene could be efficiently biodegraded when the initial benzene concentration was below 150 mg/L. The metabolites of anaerobic nitrate-dependent benzene oxidation by strain B. cereus were identified as phenol and benzoate. The results of substrate interaction between binary combinations for benzene, phenol and benzoate showed that the simultaneous presence of benzene stimulated the degradation of benzoate, whereas the addition of benzene inhibited the degradation of phenol. Benzene degradation by B. cereus was enhanced by the addition of phenol and benzoate, the enhanced effects were more pronounced at higher concentration. To our knowledge, this is the first report that the isolated bacterial culture of B. cereus can efficiently degraded benzene under nitrate reducing conditions.

Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing

The flow of carbon under sulfate-reducing conditions within a benzene-mineralizing enrichment culture was analysed using fully labelled [13C6]-benzene. Over 180 days of incubation, 95% of added 13C-benzene was released as 13C-carbon dioxide. DNA extracted from cultures that had degraded different amounts of unlabelled or 13C-labelled benzene was centrifuged in CsCl density gradients to identify 13C-benzene-assimilating organisms by density-resolved terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA gene fragments. Two phylotypes showed significantly increased relative abundance of their terminal restriction fragments in 'heavy' fractions of 13C-benzene-incubated microcosms compared with a 12C-benzene-incubated control: a member of the Cryptanaerobacter/Pelotomaculum group within the Peptococcaceae, and a phylotype belonging to the Epsilonproteobacteria. The Cryptanaerobacter/Pelotomaculum phylotype was the most frequent sequence type. A small amount of 13C-methane was aceticlastically produced, as concluded from the linear relationship between methane production and benzene degradation and the detection of Methanosaetaceae as the only methanogens present. Other phylotypes detected but not 13C-labelled belong to several genera of sulfate-reducing bacteria, that may act as hydrogen scavengers for benzene oxidation. Our results strongly support the hypothesis that benzene is mineralized by a consortium consisting of syntrophs, hydrogenotrophic sulfate reducers and to a minor extent of aceticlastic methanogens.

A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor

A bacterium (strain G5G6) that grows anaerobically with toluene was isolated from a polluted aquifer (Banisveld, the Netherlands). The bacterium uses Fe(III), Mn(IV) and nitrate as terminal electron acceptors for growth on aromatic compounds. The bacterium does not grow on sugars, lactate or acetate. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain G5G6 belonged to the Betaproteobacteria. Its closest, but only distantly related, cultured relative is Sterolibacterium denitrificans Chol-1S(T) (94.6% similarity of the 16S rRNA genes), a cholesterol-oxidizing, denitrifying bacterium. Strain G5G6 possesses the benzylsuccinate synthase A (bssA) gene encoding the alpha-subunit of Bss, which catalyzes the first step in anaerobic toluene degradation. The deduced BssA amino acid sequence is closely related to those of Azoarcus and Thauera species, which also belong to the Betaproteobacteria. Strain G5G6 is the first toluene-degrading, iron-reducing bacterium that does not belong to the Geobacteraceae within the Deltaproteobacteria. Based on phylogenetic and physiological comparison, strain G5G6 could not be assigned to a described species. Therefore, strain G5G6 (DSMZ 19032(T)=JCM 14632(T)) is a novel taxon of the Betaproteobacteria. We propose the name Georgfuchsia toluolica gen. nov., sp. nov.

Isolation and characterization of Alicycliphilus denitrificans strain BC, which grows on benzene with chlorate as the electron acceptor

A bacterium, strain BC, was isolated from a benzene-degrading chlorate-reducing enrichment culture. Strain BC degrades benzene in conjunction with chlorate reduction. Cells of strain BC are short rods that are 0.6 microm wide and 1 to 2 microm long, are motile, and stain gram negative. Strain BC grows on benzene and some other aromatic compounds with oxygen or in the absence of oxygen with chlorate as the electron acceptor. Strain BC is a denitrifying bacterium, but it is not able to grow on benzene with nitrate. The closest cultured relative is Alicycliphilus denitrificans type strain K601, a cyclohexanol-degrading nitrate-reducing betaproteobacterium. Chlorate reductase (0.4 U/mg protein) and chlorite dismutase (5.7 U/mg protein) activities in cell extracts of strain BC were determined. Gene sequences encoding a known chlorite dismutase (cld) were not detected in strain BC by using the PCR primers described in previous studies. As physiological and biochemical data indicated that there was oxygenation of benzene during growth with chlorate, a strategy was developed to detect genes encoding monooxygenase and dioxygenase enzymes potentially involved in benzene degradation in strain BC. Using primer sets designed to amplify members of distinct evolutionary branches in the catabolic families involved in benzene biodegradation, two oxygenase genes putatively encoding the enzymes performing the initial successive monooxygenations (BC-BMOa) and the cleavage of catechol (BC-C23O) were detected. Our findings suggest that oxygen formed by dismutation of chlorite can be used to attack organic molecules by means of oxygenases, as exemplified with benzene. Thus, aerobic pathways can be employed under conditions in which no external oxygen is supplied.

Combined carbon and hydrogen isotope fractionation investigations for elucidating benzene biodegradation pathways

Recently, combined carbon and hydrogen isotope fractionation investigations have emerged as a powerful tool for the characterization of reaction mechanisms relevant for the removal of organic pollutants. Here, we applied this approach in order to differentiate benzene biodegradation pathways under oxic and anoxic conditions in laboratory experiments. Carbon and hydrogen isotope fractionation of benzene was studied with four different aerobic strains using a monooxygenase or a dioxygenase for the initial benzene attack, a facultative anaerobic chlorate-reducing strain as well as a sulfate-reducing mixed culture. Carbon and hydrogen enrichment factors (epsilon(C), epsilon(H)) varied for the specific pathways and degradation conditions, respectively, so that from the individual enrichment factors only limited information could be obtained for the identification of benzene biodegradation pathways. However, using the slope derived from hydrogen vs carbon isotope discriminations or the ratio of hydrogen to carbon enrichment factors (lambda = deltaH/ deltaC approximately epsilon(H)/epsilon(C)), benzene degradation mechanisms could be distinguished. Although experimentally determined lambda values partially overlapped, ranges could be determined for different benzene biodegradation pathways. Specific lambda values were < 2 for dihydroxylation, between 7 and 9 for monohydroxylation, and > 17 for anaerobic degradation. Moreover, variations in lambda values suggest that more than one reaction mechanism exists for monohydroxylation as well as for anaerobic benzene degradation under nitrate-reducing, sulfate-reducing, or methanogenic conditions. Our results show that the combined carbon and hydrogen isotope fractionation approach has potential to elucidate biodegradation pathways of pollutants in field and laboratory microcosm studies.