Microstructure of anaerobic granules bioaugmented with Desulfitobacterium frappieri PCP-1

Mechanisms of aerobic dechlorination of hexachlorobenzene and pentachlorophenol by Nocardioides sp. PD653

We sought to elucidate the mechanisms underlying the aerobic dechlorination of the persistent organic pollutants hexachlorobenzene (HCB) and pentachlorophenol (PCP). We performed genomic and heterologous expression analyses of dehalogenase genes in Nocardioides sp. PD653, the first bacterium found to be capable of mineralizing HCB via PCP under aerobic conditions. The hcbA1A2A3 and hcbB1B2B3 genes, which were involved in catalysing the aerobic dechlorination of HCB and PCP, respectively, were identified and characterized; they were classified as members of the two-component flavin-diffusible monooxygenase family. This was subsequently verified by biochemical analysis; aerobic dechlorination activity was successfully reconstituted in vitro in the presence of flavin, NADH, the flavin reductase HcbA3, and the HCB monooxygenase HcbA1. These findings will contribute to the implementation of in situ bioremediation of HCB- or PCP-contaminated sites, as well as to a better understanding of bacterial evolution apropos their ability to degrade heavily chlorinated anthropogenic compounds under aerobic conditions.

Identification of the novel hcbB operon catalyzing the dechlorination of pentachlorophenol in the Gram-positive bacterium Nocardioides sp. strain PD653

While pcp genes are well known in Gram-negative bacteria to code for the enzymes responsible for pentachlorophenol (C₆HCl₅O; PCP) degradation, little is known about PCP-degrading genes in Gram-positive bacteria. Here we describe a novel gene operon possibly responsible for catalyzing the degradation of PCP in the Gram-positive bacterium Nocardioides sp. strain PD653, which is capable of mineralizing hexachlorobenzene (C₆Cl₆; HCB) via PCP. Transcriptome analysis based on RNA-Seq revealed overexpressed genes in strain PD653 following exposure to HCB. Based on in silico annotation, three open reading frames (ORFs) were selected as biodegrading enzyme candidates. Recombinant E. coli cells expressing candidate genes degraded approximately 9.4 µmol L^-1 PCP in 2 hr. Therefore, we designated these genes as hcbB1, hcbB2, and hcbB3. Interestingly, PCP-degrading activity was recorded when hcbB3 was coexpressed with hcbB1 or hcbB2, and the function of HcbB3 was expected to be similar to chlorophenol 4-monooxygenase (TftD).

Biodegradability of Nonionic Surfactant Used in the Remediation of Groundwaters Polluted with PCE

  The objective of this work was to evaluate the degradation of the nonionic surfactant Tween 80 by a PCE-degrading consortium anchored in bioparticles of fluidized bed bioreactors used in onsite remediation. Batch lab-scale bioreactors were set with dominant denitrifying (DN), methanogenic (M), and aerobic (Ab) metabolisms. Tween 80 at 100 mg/L was the sole source of carbon and energy. Denitrifying bioreactors had the highest surfactant removal (70%). Tween removals in M and Ab bioreactors were 53 and 37%, respectively. Removals of organic matter (COD) closely followed the efficiencies reported for Tween. This strongly suggested that degradation of Tween 80 occurred. Positive consequences of Tween degradation in remediation are first, the surfactant will not become an environmental/health liability by remaining as a recalcitrant or toxic substance in aquifers or in treated effluents; and second, savings on aeration could be achieved by conducting Tween 80 degradation in anaerobic conditions, either DN or M.

Investigation of microbial biofilm structure by laser scanning microscopy

Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.

The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1

In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic consortium for its capacity to dehalogenate pentachlorophenol (PCP) into 3-chlorophenol. This strain is also capable of dehalogenating several other chloroaromatic compounds and tetrachloroethene into trichloroethene. Four gene loci encoding putative chlorophenol-reductive dehalogenases (CprA2 to CprA5) were detected, and the products of two of these loci have been demonstrated to dechlorinate different chlorinated phenols. Strain PCP-1 was used in laboratory-scale bioprocesses to degrade PCP present in contaminated environments. Desulfitobacterium hafniense PCP-1 is an excellent candidate for the development of efficient bioprocesses to degrade organohalide compounds.

Natural strategies for the spatial optimization of metabolism in synthetic biology

Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.

Successful bacterial incorporation into activated sludge flocs using alginate

Bioaugmentation experiments with the aerobic denitrifier Microvirgula aerodenitrificans were performed in an aerobic continuous stirred tank reactor (CSTR) treating urban wastewater. The fate of the added bacteria was monitored by a specific fluorescent oligonucleotide probe targeting 16S rRNA. The first addition of the strain led to its rapid disappearance because of grazing. Bacteria were then embedded within an alginate matrix before inoculation. Alginate fragments adhered to the existing flocs and were progressively colonized by the indigenous flora. Thereafter, microcolonies of the exogenous bacterium were found to be incorporated into existing flocs.

Microeukaryote diversity in a marine methanol-fed fluidized denitrification system

The marine methanol-fed fluidized denitrification system operated by the Montreal Biodome includes carriers on which a denitrifying biofilm has developed. Previous observations showed a high abundance of microeukaryotes living in and around the biofilm. These eukaryotes may influence the system's denitrification efficiency. The composition of the microeukaryote population was determined. Microscopic observations showed at least 20 different morphologies that included large numbers of ciliates. Molecular analyses of an 18S ribosomal RNA (rDNA) gene library revealed 31 different phylotypes. Alveolobiontes were the most abundant phylotypes and made up 75% of the 159 screened clones. Other eukaryotic groups, including Stramenopiles, Fungi, Amoebozoa, and nematodes, were also present. From 18S rDNA specific sequences, one of the Amoebozoa-affiliated phylotypes was visualized by fluorescence in situ hybridization. It had a rod-like irregular shape and measured less than 5 mum in length. We determined the impact of protozoans on the denitrifying activity. In a laboratory-scale batch culture assays, the denitrifying biofilm was treated with cycloheximide and nystatin that eliminated the protozoans. No difference in the denitrification rate was found. However, planktonic bacteria were more abundant in the treated culture medium.

Application of high rate nitrifying trickling filters for potable water treatment

The interference of ammonia with chlorination is a prevalent problem encountered by water treatment plants located throughout South East Asia. The efficacy of high rate, plastic-packed trickling filters as a pre-treatment process to remove low concentrations of ammonia from polluted surface water was investigated. This paper presents the findings from a series of pilot experiments, which were designed to investigate the effect of specific conditions-namely low ammonia feed concentrations (0.5-5.0 mg NH(4)-NL(-1)), variations in hydraulic surface load (72.5-145 m(3)m(-2)d(-1)) and high suspended solid loads (51+/-25 mgL(-1))-on filter nitrifying capacity. The distribution of nitrification activity throughout a trickling filter bed was also characterised. Results confirmed that high hydraulic rate trickling filters were able to operate successfully, under ammonia-N concentrations some 10- to 50-fold lower and at hydraulic loading rates 30-100 times greater than those of conventional wastewater applications. Mass transport limitations posed by low ammonia-N concentrations on overall filter performance were insignificant, where apparent nitrification rates (0.4-1.6 g NH(4)-Nm(-2)d(-1)), equivalent to that of wastewater filters were recorded. High inert suspended solid loadings had no adverse effect on nitrification. Results imply that implementation of high rate trickling filters at the front-end of a water treatment train would reduce the ammonia-related chlorine demand, thereby offering significant cost savings.

Layered structure of bacterial and archaeal communities and their in situ activities in anaerobic granules

The microbial community structure and spatial distribution of microorganisms and their in situ activities in anaerobic granules were investigated by 16S rRNA gene-based molecular techniques and microsensors for CH(4), H(2), pH, and the oxidation-reduction potential (ORP). The 16S rRNA gene-cloning analysis revealed that the clones related to the phyla Alphaproteobacteria (detection frequency, 51%), Firmicutes (20%), Chloroflexi (9%), and Betaproteobacteria (8%) dominated the bacterial clone library, and the predominant clones in the archaeal clone library were affiliated with Methanosaeta (73%). In situ hybridization with oligonucleotide probes at the phylum level revealed that these microorganisms were numerically abundant in the granule. A layered structure of microorganisms was found in the granule, where Chloroflexi and Betaproteobacteria were present in the outer shell of the granule, Firmicutes were found in the middle layer, and aceticlastic Archaea were restricted to the inner layer. Microsensor measurements for CH(4), H(2), pH, and ORP revealed that acid and H(2) production occurred in the upper part of the granule, below which H(2) consumption and CH(4) production were detected. Direct comparison of the in situ activity distribution with the spatial distribution of the microorganisms implied that Chloroflexi contributed to the degradation of complex organic compounds in the outermost layer, H(2) was produced mainly by Firmicutes in the middle layer, and Methanosaeta produced CH(4) in the inner layer. We determined the effective diffusion coefficient for H(2) in the anaerobic granules to be 2.66 x 10(-5) cm(2) s(-1), which was 57% in water.

Large scale dielectrophoretic construction of biofilms using textile technology

Arrays of microelectrodes for AC electrokinetic experiments were fabricated by weaving together stainless steel wires (weft) and flexible polyester yarn (warp) in a plain weave pattern. The cloth produced can be used to collect cells in low conductivity media by dielectrophoresis (DEP). The construction of model biofilms consisting of a yeast layer on top of a layer of M. luteus is demonstrated, using polyethylenimine (PEI) as the flocculating agent. This technique offers an alternative to the formation of biofilms at microelectrodes made by photolithography, and would allow the construction of biofilms with defined internal architectures by DEP at much larger scales than was possible previously. Furthermore, the flexibility of the cloth would also allow it to be distorted or folded into various shapes.

The Desulfitobacterium genus

Desulfitobacterium spp. are strictly anaerobic bacteria that were first isolated from environments contaminated by halogenated organic compounds. They are very versatile microorganisms that can use a wide variety of electron acceptors, such as nitrate, sulfite, metals, humic acids, and man-made or naturally occurring halogenated organic compounds. Most of the Desulfitobacterium strains can dehalogenate halogenated organic compounds by mechanisms of reductive dehalogenation, although the substrate spectrum of halogenated organic compounds varies substantially from one strain to another, even with strains belonging to the same species. A number of reductive dehalogenases and their corresponding gene loci have been isolated from these strains. Some of these loci are flanked by transposition sequences, suggesting that they can be transmitted by horizontal transfer via a catabolic transposon. Desulfitobacterium spp. can use H2 as electron donor below the threshold concentration that would allow sulfate reduction and methanogenesis. Furthermore, there is some evidence that syntrophic relationships occur between Desulfitobacterium spp. and sulfate-reducing bacteria, from which the Desulfitobacterium cells acquire their electrons by interspecies hydrogen transfer, and it is believed that this relationship also occurs in a methanogenic consortium. Because of their versatility, desulfitobacteria can be excellent candidates for the development of anaerobic bioremediation processes. The release of the complete genome of Desulfitobacterium hafniense strain Y51 and information from the partial genome sequence of D. hafniense strain DCB-2 will certainly help in predicting how desulfitobacteria interact with their environments and other microorganisms, and the mechanisms of actions related to reductive dehalogenation.

Is bioaugmentation a feasible strategy for pollutant removal and site remediation?

Microorganisms can degrade numerous organic pollutants owing to their metabolic machinery and to their capacity to adapt to inhospitable environments. Thus, microorganisms are major players in site remediation. However, their efficiency depends on many factors, including the chemical nature and the concentration of pollutants, their availability to microorganisms, and the physicochemical characteristics of the environment. The capacity of a microbial population to degrade pollutants within an environmental matrix (e.g. soil, sediment, sludge or wastewater) can be enhanced either by stimulation of the indigenous microorganisms by addition of nutrients or electron acceptors (biostimulation) or by the introduction of specific microorganisms to the local population (bioaugmentation). Although it has been practiced in agriculture and in wastewater treatment for years, bioaugmentation is still experimental. Many factors (e.g. predation, competition or sorption) conspire against it. However, several strategies are currently being explored to make bioaugmentation a successful technology in sites that lack significant populations of biodegrading microorganisms. Under optimal local conditions, the rate of pollutant degradation might increase upon addition of an inoculant to remediate a chemical spill; however, the most successful cases of bioaugmentation occur in confined systems, such as bioreactors in which the conditions can be controlled to favour survival and prolonged activity of the exogenous microbial population.

Desulfitobacterium hafniense is present in a high proportion within the biofilms of a high-performance pentachlorophenol-degrading, methanogenic fixed-film reactor

We developed a pentachlorophenol (PCP)-degrading, methanogenic fixed-film reactor by using broken granular sludge from an upflow anaerobic sludge blanket reactor. This methanogenic consortium was acclimated with increasing concentrations of PCP. After 225 days of acclimation, the reactor was performing at a high level, with a PCP removal rate of 1,173 muM day(-1), a PCP removal efficiency of up to 99%, a degradation efficiency of approximately 60%, and 3-chlorophenol as the main chlorophenol residual intermediate. Analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that Bacteria and Archaea in the reactor stabilized in the biofilms after 56 days of operation. Important modifications in the profiles of Bacteria between the original granular sludge and the reactor occurred, as less than one-third of the sludge DGGE bands were still present in the reactor. Fluorescence in situ hybridization experiments with probes for Archaea or Bacteria revealed that the biofilms were composed mostly of Bacteria, which accounted for 70% of the cells. With PCR species-specific primers, the presence of the halorespiring bacterium Desulfitobacterium hafniense in the biofilm was detected very early during the reactor acclimation period. D. hafniense cells were scattered in the biofilm and accounted for 19% of the community. These results suggest that the presence of PCP-dehalogenating D. hafniense in the biofilm was crucial for the performance of the reactor.

Distribution of EPS and cell surface hydrophobicity in aerobic granules

This study described the distribution of extracellular polysaccharides (EPS) and hydrophobicity in aerobic granule as well as the essential role of EPS in maintaining the stable structure of aerobic granules. Aerobic granules showed a heterogeneous structure, which had an outer shell with high biomass density and an inner core having a relatively low biomass density. Results showed that the outer shell of aerobic granule was composed of poorly soluble and noneasily biodegradable EPS, whereas its core part was filled with readily soluble and biodegradable EPS. It was further found that the shell of aerobic granule exhibited a higher hydrophobicity than the core of granule. The insoluble EPS present in the granule shell would play a protective role with respect to the structure stability and integrity of aerobic granules.

Towards microbial tissue engineering?

Tissue engineering involves the creation of multicellular tissues from individual cells. It was previously perceived that tissues were only formed by higher organisms such as plants and animals. However, it is now known that multicellular systems of microorganisms, such as microbial colonies, biofilms, flocs and aggregates, can also show extensive spatial organization. Here, we discuss methods that can be used to spatially organize microorganisms--bacteria, in particular--into tissue-like materials with defined internal architectures. Some potential uses of such "microbial tissues" are covered.

Anaerobic microbial dehalogenation

The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating--or completely mineralizing--halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.

Effect of ammonia on the methanogenic activity of methylaminotrophic methane producing Archaea enriched biofilm

Ammonia is a metabolic product in the decomposition of protein wastes, and has a recognized inhibitory effect on methanogenesis; this effect has been slightly quantified on methanogenic biofilms and particularly those populated by methanogenic Archaea which produce ammonia as a catabolic product from methylated amines. This paper presents studies on the effect of ammonia on maximum methanogenic activity of anaerobic biofilms enriched by methylaminotrophic methane producing Archaea (mMPA). The effect of unionized free ammonia on the specific maximum methanogenic activity of a mMPA enriched biofilm was studied, using 250 mL flasks containing ceramic rings colonized by 30 day-old experimental biofilm and adding 48.8 (control system), 73.8, 98.8, 148.8, 248.8, 448.8 and 848.8 mg NH(3)-N/L. The systems were maintained for ten days at a pH of 7.5 and temperature of 37 degrees C. The results showed that at 848.8 mg NH(3)-N/L, biofilm methane production required 36 h adaptation period, prior to entering into maximum production phase. The highest maximum methanogenic activity reached a value of 2.337+/-0.213 g COD methane/g VSS *day when 48.8 mg NH(3)-N/L was added, and inhibition was clearly observed in those systems above 148.8 mg NH(3)-N/L, producing under 1.658+/-0.185 g COD methane/g VSS *day. The lowest methanogenic activity reached was 0.639+/-0.162 g COD methane/g VSS *day at the system added with 848.8 mg NH(3)-N/L. When applying the Luong and non-competitive inhibition models, the best fit was obtained with the non-competitive model, which predicted 50% inhibition of methanogenic activity at 365.288 mg NH(3)-N/L.

High-rate sulfate reduction at high salinity (up to 90 mS.cm?1) in mesophilic UASB reactors

Sulfate reduction in salt-rich wastewaters using unadapted granular sludge was investigated in 0.9 L UASB reactors (pH 7.0 +/- 0.2; hydraulic retention time from 8-14 h) fed with acetate, propionate, or ethanol at organic loading rates up to 10 gCOD x L(-1) x day(-1) and in excess sulfate (COD/SO(4) (2-) of 0.5). High-rate sulfate reduction rates (up to 3.7 gSO(4) (2-) x L(-1).day(-1)) were achieved at salinities exceeding 50 gNaCl.L(-1) and 1 gMgCl(2) x L(-1). Sulfate reduction proceeded at a salinity of up to 70 gNaCl x L(-1) and 1 gMgCl(2) x L(-1) (corresponding to a conductivity of about 85-90 mS x cm(-1)), although at lower rates compared to a conductivity of 60-70 mS x cm(-1). Ethanol as well as propionate were suitable substrates for sulfate reduction, with acetate and sulfide as the end products. The successful high-rate treatment was due to the proliferation of a halotolerant incomplete oxidizing SRB population present in the unadapted inoculum sludge. Bioaugmentation of this sludge with the acetate oxidizing halotolerant SRB Desulfobacter halotolerans was unsuccessful, as the strain washed out from the UASB reactor without colonizing the UASB granules.