Anaerobic methyl tert-butyl ether-degrading microorganisms identified in wastewater treatment plant samples by stable isotope probing

A review on co-metabolic degradation of organic micropollutants during anaerobic digestion: Linkages between functional groups and digestion stages

The emerging presence of organic micropollutants (OMPs) in water bodies produced by human activities is a source of growing concern due to their environmental and health issues. Biodegradation is a widely employed treatment method for OMPs in wastewater owing to its high efficiency and low operational cost. Compared to aerobic degradation, anaerobic degradation has numerous advantages, including energy efficiency and superior performance for certain recalcitrant compounds. Nonetheless, the low influent concentrations of OMPs in wastewater treatment plants (WWTPs) and their toxicity make it difficult to support the growth of microorganisms. Therefore, co-metabolism is a promising mechanism for OMP biodegradation in which co-substrates are added as carbon and energy sources and stimulate increased metabolic activity. Functional microorganisms and enzymes exhibit significant variations at each stage of anaerobic digestion affecting the environment for the degradation of OMPs with different structural properties, as these factors substantially influence OMPs' biodegradability and transformation pathways. However, there is a paucity of literature reviews that explicate the correlations between OMPs' chemical structure and specific metabolic conditions. This study provides a comprehensive review of the co-metabolic processes which are favored by each stage of anaerobic digestion and attempts to link various functional groups to their favorable degradation pathways. Furthermore, potential co-metabolic processes and strategies that can enhance co-digestion are also identified, providing directions for future research.

Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances

Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.

Influence of iron (hydr)oxide mineralogy and contents in aquifer sediments on dissolved organic carbon attenuations during aquifer storage and recovery

Aquifer storage and recovery (ASR) is a promising approach for managing water resources that enhances water quality through biogeochemical reactions occurring within aquifers. Iron (hydr)oxides, which are the predominant metallic oxides in soil, play a crucial role in degrading dissolved organic carbon (DOC), primarily through a process known as dissimilatory iron reduction (DIR). However, the efficiency of this reaction varies depending on the mineralogy and composition of the aquifer, and this understanding is essential for adequate water quality in ASR. The objective of this study is to investigate the impact of iron (hydr)oxide on acetate, as an organic carbon source, attenuation during the ASR. To achieve this, three sets of laboratory sediment columns were prepared, each containing a different type of iron (hydr)oxide minerals: ferrihydrite, goethite, and hematite. Following an acclimation period of 28 days to simulate the microcosm within an aquifer, the columns were continuously supplied with the simulated river water spiked with acetate (DOC 40-60 mg L-1), and the acetate concentration in the effluent was monitored. The result revealed that the column containing ferrihydrite achieved 97% acetate attenuation through DIR with anoxic conditions (DO < 0.1 mg L-1), while the goethite and hematite columns exhibited limited attenuation rates of 40 and 50%, respectively. Furthermore, the efficiency of acetate attenuation in the ferrihydrite columns increased with the content of ferrihydrite but experienced a rapidly declined at higher contents (3-4%), possibly due to the partial conversion of ferrihydrite to goethite as a result of the interaction between ferrihydrite and the Fe(II) produced during DIR. Additionally, an analysis of the microbial community demonstrated that microorganisms known to possess the ability to reduce iron (hydr)oxides under anaerobic conditions were abundant in the ferrihydrite columns.

Potential of stable isotope analysis to deduce anaerobic biodegradation of ethyl tert-butyl ether (ETBE) and tert-butyl alcohol (TBA) in groundwater: a review

Understanding anaerobic biodegradation of ether oxygenates beyond MTBE in groundwater is important, given that it is replaced by ETBE as a gasoline additive in several regions. The lack of studies demonstrating anaerobic biodegradation of ETBE, and its product TBA, reflects the relative resistance of ethers and alcohols with a tertiary carbon atom to enzymatic attack under anoxic conditions. Anaerobic ETBE- or TBA-degrading microorganisms have not been characterized. Only one field study suggested anaerobic ETBE biodegradation. Anaerobic (co)metabolism of ETBE or TBA was reported in anoxic microcosms, indicating their biodegradation potential in anoxic groundwater systems. Non-isotopic methods, such as the detection of contaminant loss, metabolites, or ETBE- and TBA-degrading bacteria are not sufficiently sensitive to track anaerobic biodegradation in situ. Compound- and position-specific stable isotope analysis provides a means to study MTBE biodegradation, but isotopic fractionation of ETBE has only been studied with a few aerobic bacteria (εC -0.7 to -1.7‰, εH -11 to -73‰) and at one anoxic field site (δ2H-ETBE +14‰). Similarly, stable carbon isotope enrichment (δ13C-TBA +6.5‰) indicated TBA biodegradation at an anoxic field site. CSIA and PSIA are promising methods to detect anaerobic ETBE and TBA biodegradation but need to be investigated further to assess their full potential at field scale.

Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms

Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for ¹³C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for ¹³C-1,4-dioxane assimilation. The dominant enriched phylotypes for ¹³C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.

Biodegradation and fate of ethyl tert-butyl ether (ETBE) in soil and groundwater: A review

This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.

Metabolic Functional Community Diversity of Associated Bacteria during the Degradation of Phytoplankton from a Drinking Water Reservoir

In the drinking water reservoir ecosystem, phytoplankton and bacteria play important roles in shaping freshwater health and function. In this work, the associated bacterial community functional diversity during degradation of phytoplankton was determined using the substrate utilization profiling (BIOLOG) technique, meanwhile, the composition and concentration of phytoplankton were examined using a microscope. The results indicated that Euglena decreased 58.33% from 0 to 38 d, while the smallest degradation of Bacillariophyta was 20.19%. Average well color development (AWCD_590nm) increased during the static periods from 0 to 38 d; however, the AWCD_590nm of 18 and 38 d had no significant difference (p < 0.05). The Simpson’s index (D) was in accordance with Shannon’s diversity (H) and species richness(S); it was measured to be18 > 38 > 5 > 0 d. There were significant differences in the pattern and level of carbon sources used by the phytoplankton-associated bacteria. In addition, the principle component analyses (PCA) suggested that the first principle component (PC1) and the second principle component (PC2) explained 46.76% and 21.49% of the total variation for bacterial community, respectively. Redundancy analysis (RDA) revealed that cell abundance of phytoplankton was negatively correlated with the AWCD_590nm, amino acids and other functional indexes. Therefore, the data suggest that there are differences in the phytoplankton-associated bacterial community functional diversity during different static stages of water samples collected from the drinking water reservoir.

Long-term exogenous addition of synthetic acyl homoserine lactone enhanced the anaerobic granulation process

Although adding long-term acyl homoserine lactone (AHL) over one month was highly instructive for the development of an AHL-based anaerobic granulation strategy, the role of long-term exogenous AHL at different concentrations in the granulation process was poorly understood due to commercial exogenous AHL's extremely high cost. In this study, organic synthesis of N-decanoyl-homoserine lactone (C10-HSL) was employed for the first time to drastically reduce the cost of the AHL addition. Daily dosages of exogenous C10-HSL at 50 nM, 500 nM and 5000 nM were separately added into anaerobic bioreactors to promote the granulation process for as long as 168 days. 50 nM C10-HSL showed a negligible effect on the granulation process while 5000 nM C10-HSL achieved the best performance with the highest chemical oxygen demand (COD) removal, largest granule size and best extracellular polymeric substance production. Bacterial analysis indicated that exogenous C10-HSL showed a concentration-related effect in bacterial community organization. Besides, addition of 5000 nM C10-HSL resulted in the greatest promotion of Methanosaeta which was extremely important to the formation of anaerobic granule. This study provides a foundation for the future application of long-term exogenous AHL manipulation to improve the granulation process in an engineered ecosystem.

DNA-SIP Reveals the Diversity of Chemolithoautotrophic Bacteria Inhabiting Three Different Soil Types in Typical Karst Rocky Desertification Ecosystems in Southwest China

Autotrophs that inhabit soils receive less attention than their counterparts in other ecosystems, such as deep-sea and subsurface sediments, due to the low abundance of autotrophs in soils with high organic contents. However, the karst rocky desertification region is a unique ecosystem that may have a low level of organic compounds. Therefore, we propose that karst rocky desertification ecosystems may harbor diverse autotrophic microbial communities. In this study, DNA-SIP was employed to identify the chemolithoautotrophic bacteria inhabiting three soil types (i.e., grass, forest, and agriculture) of the karst rocky desertification ecosystems. The results indicated that potential chemolithoautotrophic population was observed in each soil type, even at different time points after amending ¹³C-NaHCO₃, confirming our hypothesis that diverse autotrophs contribute to the carbon cycle in karst soils. Bacteria, such as Ralstonia, Ochrobactrum, Brevibacterium, Acinetobacter, and Corynebacterium, demonstrated their potential to assimilate inorganic carbon and reduce nitrate or thiosulfate as electron acceptors. Putative mixotrophs were identified by DNA-SIP as well, suggesting the metabolic versatility of soil microbiota. A co-occurrence network further indicated that autotrophs and heterotrophs may form associated communities to sustain the ecosystem function. Our current study revealed the metabolic diversity of autotrophic bacteria in soil habitats and demonstrated the potentially important role of chemoautotrophs in karst rocky desertification ecosystems.

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.

Bioaugmentation for treatment of full-scale diethylene glycol monobutyl ether (DGBE) wastewater by Serratia sp. BDG-2

A novel bacterial strain BDG-2 was isolated and used to augment the treatment of silicon plate manufacturing wastewater that primarily contains diethylene glycol monobutyl ether (DGBE). BDG-2 was identified as a Serratia sp. Under the optimal conditions of 30 °C, pH 9 and DGBE concentration of 2000 mg L(-1), the bioaugmented system achieved 96.92% COD removal after 39.9h. Laboratory-scale technological matching results indicated that, in a biofilm process with the addition of 100 mg L(-1) ammonia and 5 mg L(-1) total phosphorus (TP), 70.61% COD removal efficiency could be obtained in 46 h. Addition of polyaluminium chloride (PAC) to the reactors during the suspension process enhanced the settleability of the BDG-2 culture. Subsequently, successful start-up and stable operation of a full-scale bioaugmented treatment facilities were accomplished, and the volumetric organic load in the plug-flow aeration tank was 2.17 ± 0.81 kg m(-3) d(-1). The effluent COD of the facilities was stable and always below 100 mg L(-1).

Identification of a Ruminococcaceae Species as the Methyl tert-Butyl Ether (MTBE) Degrading Bacterium in a Methanogenic Consortium

The widespread use of methyl tert-butyl ether (MTBE) has caused major contamination of groundwater sources and is a concern due to its taste and odor problems, as well as its toxicity. MTBE can be degraded anaerobically which makes bioremediation of contaminated aquifers a potential solution. Nevertheless, the organisms and mechanisms that are responsible for anaerobic MTBE degradation are still unknown. The aim of our research was to identify the organisms actively degrading MTBE. For this purpose we characterized an anaerobic methanogenic culture enriched with MTBE as the sole carbon source from the New Jersey Arthur Kill intertidal strait sediment. The cultures were analyzed using stable isotope probing (SIP) combined with terminal restriction fragment length polymorphism (T-RFLP), high-throughput sequencing and clone library analysis of bacterial 16S rRNA genes. The sequence data indicated that phylotypes belonging to the Ruminococcaceae in the Firmicutes were predominant in the methanogenic cultures. SIP experiments also showed sequential incorporation of the (13)C labeled MTBE by the bacterial community with a bacterium most closely related to Saccharofermentans acetigenes identified as the bacterium active in O-demethylation of MTBE. Identification of the microorganisms responsible for the activity will help us better understand anaerobic MTBE degradation processes in the field and determine biomarkers for monitoring natural attenuation.

Extracellular polymeric substances for Zn (II) binding during its sorption process onto aerobic granular sludge

The aim of this study was to evaluate the interaction between extracellular polymeric substances (EPS) and Zn (II) during the sorption process of Zn (II) onto aerobic granular sludge. Batch results showed that the adsorption rate of Zn (II) onto aerobic granular sludge was better fitted with pseudo-second order kinetics model, and the adsorption isotherm data agreed well with Freundlich equation. Extracellular polymeric substances (EPS) for Zn (II) binding during sorption process was investigated by using a combination of three-dimensional excitation-emission matrix (3D-EEM), synchronous fluorescence spectra, two-dimensional correlation spectroscopy (2D-COS) and Fourier transform infrared spectroscopy (FTIR). Results implied that the main composes of EPS, including polysaccharide (PS) and protein (PN), decreased from 5.92±0.13 and 23.55±0.76 mg/g SS to 4.11±0.09 and 9.55±0.68 mg/g SS after the addition of different doses of Zn (II). 3D-EEM showed that the intensities of PN-like substances and humic-like substances were obviously decreased during the sorption process. According to synchronous fluorescence spectra, the quenching mechanism between PN-like substances and Zn (II) was mainly caused by a static quenching process. Additionally, 2D-COS indicated that PN-like substances were more susceptible to Zn (II) binding than humic-like substances. It was also found that the main functional groups for complexation of Zn (II) and EPS were OH groups, N-H groups and C=O stretching vibration. The findings of this study are significant to reveal the fate of heavy metal during its sorption process onto aerobic granular sludge through EPS binding, and provide useful information on the interaction between EPS and heavy metal.

Multi-substrate biodegradation interaction of 1, 4-dioxane and BTEX mixtures by Acinetobacter baumannii DD1

This study evaluated substrate interactions during the aerobic biodegradation of 1, 4-dioxane and BTEX mixtures by a pure culture, Acinetobacter baumannii DD1, which is capable of utilizing 1, 4-dioxane for growth. A. baumannii DD1 could utilize BTEX as a sole carbon source, but could not utilize m-xylene and p-xylene. In binary mixtures, there was a lag of about 14 h before the degradation of BTE, and 1, 4-dioxane only started to be utilized when BTE was completely degraded by 1, 4-dioxane-grown DD1. Furthermore, the biodegradation rate of 1, 4-dioxane decreased from 73.33 to 40.74 mg/(h g dry weight) after the biodegradation of benzene. 1, 4-dioxane could not be degraded after the biodegradation of o-xylene in 80 h. DD1 could also not degrade m-xylene and p-xylene coexisting with 1, 4-dioxane. The ability of DD1 to degrade BTEX occurred in the following order: benzene > ethylbenzene > toluene > o-xylene > m-xylene = p-xylene. The biodegradation of 1, 4-dioxane was not activated in the mixture with o-xylene, primarily because of the accumulation of the specific toxic intermediate, 2, 3-dimethylphenol. The lag in BTE degradation was presumably because of the induction of enzymes necessary for BTE degradation. Additionally, SDS-PAGE analysis demonstrated that there were different proteins during the degradation of benzene and 1, 4-dioxane.

The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing

Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of (13)CH4 and (13)CO2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

Indoor Heating Drives Water Bacterial Growth and Community Metabolic Profile Changes in Building Tap Pipes during the Winter Season

The growth of the bacterial community harbored in indoor drinking water taps is regulated by external environmental factors, such as indoor temperature. However, the effect of indoor heating on bacterial regrowth associated with indoor drinking water taps is poorly understood. In the present work, flow cytometry and community-level sole-carbon-source utilization techniques were combined to explore the effects of indoor heating on water bacterial cell concentrations and community carbon metabolic profiles in building tap pipes during the winter season. The results showed that the temperature of water stagnated overnight ("before") in the indoor water pipes was 15-17 °C, and the water temperature decreased to 4-6 °C after flushing for 10 min ("flushed"). The highest bacterial cell number was observed in water stagnated overnight, and was 5-11 times higher than that of flushed water. Meanwhile, a significantly higher bacterial community metabolic activity (AWCD590nm) was also found in overnight stagnation water samples. The significant "flushed" and "taps" values indicated that the AWCD590nm, and bacterial cell number varied among the taps within the flushed group (p < 0.01). Heatmap fingerprints and principle component analyses (PCA) revealed a significant discrimination bacterial community functional metabolic profiles in the water stagnated overnight and flushed water. Serine, threonine, glucose-phosphate, ketobutyric acid, phenylethylamine, glycerol, putrescine were significantly used by "before" water samples. The results suggested that water stagnated at higher temperature should be treated before drinking because of bacterial regrowth. The data from this work provides useful information on reasonable utilization of drinking water after stagnation in indoor pipes during indoor heating periods.

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site

This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

Toxicity assessment of 4-chlorophenol to aerobic granular sludge and its interaction with extracellular polymeric substances

The main objective of this study was to evaluate the toxicity of 4-chlorophenol (4-CP) to aerobic granular sludge in the process of treating ammonia rich wastewater. In the short-term exposure of 4-CP of 5 and 10 mg/L, ammonia nitrogen removal efficiencies in the batch reactors decreased to 87.18±2.81 and 41.16±3.55%, which were remarkably lower than that of control experiment (99.83±0.54%). Correspondingly, the respirometric activities of heterotrophic and autotrophic bacteria of aerobic granular sludge were significantly inhibited in the presence of 4-CP. Moreover, the main components of extracellular polymeric substances (EPS) including polysaccharides and proteins increased from 18.74±0.29 and 22.57±0.34 mg/g SS to 27.79±0.51 and 24.69±0.38 mg/g SS, respectively, indicating that the presence of 4-CP played an important role on the EPS production. Three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy further showed that the intensities of EPS samples were obviously quenched with the increased of 4-CP concentrations. To be more detailed, synchronous fluorescence spectra indicated that the interaction between EPS and 4-CP was mainly caused by tryptophan residues. The mechanism of fluorescence quenching belongs to static quenching with a formation constant (KA) of 0.07×10(4) L/mol, implying the strong formation of EPS and 4-CP complex. The results could provide reliable and accurate information to determine the potential toxicity of 4-CP on the performance of aerobic granular sludge system.

Composition of bacterial and archaeal communities during landfill refuse decomposition processes

Little is known about the archaeal and the bacterial diversities in a landfill during different phases of decomposition. In this study, the archaeal and the bacterial diversities of Laogang landfill (Shanghai, China) at two different decomposition phases (i.e., initial methanogenic phase (IMP) and stable methanogenic phase (SMP)), were culture-independently examined using PCR-based 454 pyrosequencing. A total of 47,753 sequences of 16S rRNA genes were retrieved from 69,954 reads and analyzed to evaluate the diversities of the archaeal and bacterial communities. The most predominant types of archaea were hydrogenotrophic Methanomicrobiales, and of bacteria were Proteobacteria, Firmicutes, and Bacteroidetes. As might be expected, their abundances varied at decomposition phases. Archaea Methanomicrobiales accounts for 97.6% of total archaeal population abundance in IMP and about 57.6% in SMP. The abundance of archaeal genus Halobacteriale was 0.1% in IMP and was 20.3% in the SMP. The abundance of Firmicutes was 21.3% in IMP and was 4.3% in SMP. The abundance of Bacteroidetes represented 11.5% of total bacterial in IMP and was dominant (49.4%) in SMP. Both the IMP and SMP had unique cellulolytic bacteria compositions. IMP consisted of members of Bacillus, Fibrobacter, and Eubacterium, while SMP harbored groups of Microbacterium. Both phases had Clostridium with different abundance, 4-5 folds higher in SMP.

Evaluation of ethyl tert-butyl ether biodegradation in a contaminated aquifer by compound-specific isotope analysis and in situ microcosms

Ethyl tert-butyl ether (ETBE) is an upcoming groundwater pollutant in Europe whose environmental fate has been less investigated, thus far. In the present study, we investigated the in situ biodegradation of ETBE in a fuel-contaminated aquifer using compound-specific stable isotope analysis (CSIA), and in situ microcosms in combination with total lipid fatty acid (TLFA)-stable isotope probing (SIP). In a first field investigation, CSIA revealed insignificant carbon isotope fractionation, but low hydrogen isotope fractionation of up to +14‰ along the prevailing anoxic ETBE plume suggesting biodegradation of ETBE. Ten months later, oxygen injection was conducted to enhance the biodegradation of petroleum hydrocarbons (PH) at the field site. Within the framework of this remediation measure, in situ microcosms loaded with [(13)C6]-ETBE (BACTRAP(®)s) were exposed for 119 days in selected groundwater wells to assess the biodegradation of ETBE by TLFA-SIP under the following conditions: (i) ETBE as main contaminant; (ii) ETBE as main contaminant subjected to oxygen injection; (iii) ETBE plus other PH; (iv) ETBE plus other PH subjected to oxygen injection. Under all conditions investigated, significant (13)C-incorporation into microbial total lipid fatty acids extracted from the in situ microcosms was found, providing clear evidence of ETBE biodegradation.

Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing

BACKGROUND

The sediment hosts a variety of fungal species in water supply reservoirs; however, the taxonomically and functionally diverse fungal populations have remained vastly unexplored. Here, quantitative PCR (qPCR) and recently developed high-throughput 454 GS FLX pyrosequencing were combined to investigate the abundance and diversity of sediment fungal communities in three water supply reservoirs.

RESULTS

These results revealed 1991, 2473, and 2610 copies of the 18S rRNA gene in the sediments from the ZC, SBY, and JP reservoirs, respectively. The fungal abundance in JP reservoir was 1.31 times higher than that of the ZC reservoir. In general, 43123 reads were recovered, corresponding to 945 distinct molecular operational taxonomic units (OTUs, 97% similarity cut-off level). The majority of the fungal nuclear ribosomal internal transcribed spacer (ITS) region sequences were affiliated with Ascomycota, Chytridiomycota, Basidiomycota, Glomeromycota, and Mucoromycotina. The highest Chao 1 index (962) was observed in the JP reservoir, and this value was 5.66 times greater than that of the SBY reservoir. Heat map analysis showed that Rhizophydium (relative frequency 30.98%), Placidium (20.20%), Apophysomyces (8.43%), Allomyces (6.26%), and Rhodotorula (6.01%) were the dominant genera in the JP reservoir, while Elaphomyces (20.0%) was the dominant genus in the ZC reservoir and Rhizophydium (30.98%) and Mattirolomyces (39.40%) were the most abundant in the JP and SBY reservoirs. Glomus sp. was only found in the JP reservoir. Furthermore, the larger proportions of "unassigned fungi" call for crafting International Nucleotide Sequence Database. Principle component analysis (PCA) and network analysis also suggested that tremendously diverse functional fungal populations were resident in the sediments of the three water supply reservoirs.

CONCLUSIONS

Thus, the results of this research suggest that the combination of high-throughput Roche 454 GS FLX pyrosequencing and qPCR is successfully employed to decrypt reservoir sediment fungal communities. Diverse fungi occur widely in the sediments of water supply reservoirs. These findings will undoubtedly broaden our understanding of reservoir sediment fungal species harbored in this freshwater stressful environmental condition. Future research should be conducted to determine the potential for fungi to degrade complex pollutants and their secondary metabolites related to the water quality.

Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas

Alkanes and polycyclic aromatic hydrocarbons (PAHs) are the commonly detected petroleum hydrocarbon contaminants in soils in oil exploring areas. Hydrocarbon-degrading genes are useful biomarks for estimation of the bioremediation potential of contaminated sites. However, the links between environmental factors and the distribution of alkane and PAH metabolic genes still remain largely unclear. The present study investigated the abundances and diversities of soil n-alkane and PAH-degrading bacterial communities targeting both alkB and nah genes in two oil exploring areas at different geographic regions. A large variation in the abundances and diversities of alkB and nah genes occurred in the studied soil samples. Various environmental variables regulated the spatial distribution of soil alkane and PAH metabolic genes, dependent on geographic location. The soil alkane-degrading bacterial communities in oil exploring areas mainly consisted of Pedobacter, Mycobacterium, and unknown alkB-harboring microorganisms. Moreover, the novel PAH-degraders predominated in nah gene clone libraries from soils of the two oil exploring areas. This work could provide some new insights towards the distribution of hydrocarbon-degrading microorganisms and their biodegradation potential in soil ecosystems.

Using DNA-Stable Isotope Probing to Identify MTBE- and TBA-Degrading Microorganisms in Contaminated Groundwater

Although the anaerobic biodegradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) has been documented in the laboratory and the field, knowledge of the microorganisms and mechanisms involved is still lacking. In this study, DNA-stable isotope probing (SIP) was used to identify microorganisms involved in anaerobic fuel oxygenate biodegradation in a sulfate-reducing MTBE and TBA plume. Microorganisms were collected in the field using Bio-Sep® beads amended with ¹³C₅-MTBE, ¹³C₁-MTBE (only methoxy carbon labeled), or¹³C₄-TBA. ¹³C-DNA and ¹²C-DNA extracted from the Bio-Sep beads were cloned and 16S rRNA gene sequences were used to identify the indigenous microorganisms involved in degrading the methoxy group of MTBE and the tert-butyl group of MTBE and TBA. Results indicated that microorganisms were actively degrading ¹³C-labeled MTBE and TBA in situ and the ¹³C was incorporated into their DNA. Several sequences related to known MTBE- and TBA-degraders in the Burkholderiales and the Sphingomonadales orders were detected in all three¹³C clone libraries and were likely to be primary degraders at the site. Sequences related to sulfate-reducing bacteria and iron-reducers, such as Geobacter and Geothrix, were only detected in the clone libraries where MTBE and TBA were fully labeled with ¹³C, suggesting that they were involved in processing carbon from the tert-butyl group. Sequences similar to the Pseudomonas genus predominated in the clone library where only the methoxy carbon of MTBE was labeled with ¹³C. It is likely that members of this genus were secondary degraders cross-feeding on ¹³C-labeled metabolites such as acetate.

Biodegradation of gasoline ether oxygenates

Ether oxygenates such as methyl tertiary butyl ether (MTBE) are added to gasoline to improve fuel combustion and decrease exhaust emissions. Ether oxygenates and their tertiary alcohol metabolites are now an important group of groundwater pollutants. This review highlights recent advances in our understanding of the microorganisms, enzymes and pathways involved in both the aerobic and anaerobic biodegradation of these compounds. This review also aims to illustrate how these microbiological and biochemical studies have guided, and have helped refine, molecular and stable isotope-based analytical approaches that are increasingly being used to detect and quantify biodegradation of these compounds in contaminated environments.