Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Metabolic engineering of Escherichia coli for efficient degradation of 4-fluorophenol

As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation

Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.

Bioaugmentation and its application in wastewater treatment: A review

Bioaugmentation (the process of adding selected strains/mixed cultures to wastewater reactors to improve the catabolism of specific compounds, e.g. refractory organics, or overall COD) is a promising technique to solve practical problems in wastewater treatment plants, and enhance removal efficiency. The potential of this option can now be enhanced in order to take advantage of important advances in the fields of microbial ecology, molecular biology, immobilization techniques and advanced bioreactor design. Reports on bioaugmentation in WWT show the difficulties in evaluating the potential parameters involved, leading frequently to inconclusive outcomes. Many studies have been carried out on the basis of trial-and-error approaches, and it has been reported that reactors bioaugmented with pure cultures often fail to perform as well as the pure cultures under laboratory conditions. As an interesting technical challenge, the feasibility of bioaugmentation should ultimately be assessed by data from field implementation, and this review highlights several promising areas to explore in the future.

Novel Strategy for Tracking the Microbial Degradation of Azo Dyes with Different Polarities in Living Cells

Direct visualization evidence is important for understanding the microbial degradation mechanisms. To track the microbial degradation pathways of azo dyes with different polar characterizations, sensors based on the fluorescence resonance energy transfer (FRET) from 1,8-naphthalimide to azo dyes were synthesized, in which the quenched fluorescence will recover when the azo bond was cleaved. In living cells, the sensor-tracking experiment showed that the low polarity and hydrophobic azo dye can be taken up into the cells and reduced inside the cells, whereas the high polarity and hydrophilic azo dye can be reduced only outside the cells because of the selective permeability of the cell membranes. These results indicated that there were two different bacterial degradation pathways available for different polarity azo dyes. To our knowledge, no fluorescent sensor has yet been designed for illuminating the microbial degradation mechanisms of organic pollutants with different characteristics.

Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study

The objectives of this pilot-scale study were to (1) evaluate the effectiveness of bioremediation of trichloroethylene (TCE)-contaminated groundwater with the supplement of slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, surfactants) under reductive dechlorinating conditions, (2) apply gene analyses to confirm the existence of TCE-dechlorinating genes, and (3) apply the real-time polymerase chain reaction (PCR) to evaluate the variations in TCE-dechlorinating bacteria (Dehalococcoides spp.). Approximately 350L of SPRS solution was supplied into an injection well (IW) and groundwater samples were collected and analyzed from IW and monitor wells periodically. Results show that the SPRS caused a rapid increase of the total organic carbon concentration (up to 5794mg/L), and reductive dechlorination of TCE was significantly enhanced. TCE dechlorination byproducts were observed and up to 99% of TCE removal (initial TCE concentration=1872μg/L) was observed after 50 days of operation. The population of Dehalococcoides spp. increased from 4.6×10(1) to 3.41×10(7)cells/L after 20 days of operation. DNA sequencing results show that there were 31 bacterial species verified, which might be related to TCE biodegradation. Results demonstrate that the microbial analysis and real-time PCR are useful tools to evaluate the effectiveness of TCE reductive dechlorination.

Bioaugmentation on decolorization of C.I. Direct Blue 71 by using genetically engineered strain Escherichia coli JM109 (pGEX-AZR)

The study showed that Escherichia coli JM109 (pGEX-AZR), the genetically engineered microorganism (GEM) with higher ability to decolorize azo dyes, bioaugmented successfully the dye wastewater bio-treatment systems to enhance C.I. Direct Blue 71 (DB 71) decolorization. The control and bioaugmented reactors failed at a around pH 5.0. However, the bioaugmented one succeeded at around pH 9.0, the influent DB 71 concentration was 150 mg/L, DB 71 concentration was decreased to 27.4 mg/L in 12h. The 1-3% NaCl concentration of bioaugmented reactors had no definite influence on decolorization, DB 71 concentration was decreased to 12.6 mg/L in 12h. GEM was added into anaerobic sequencing batch reactors (AnSBRs) to enhance DB 71 decolorization. Continuous operations of the control and bioaugmented AnSBRs showed that E. coli JM109 (pGEX-AZR) could bioaugment decolorization. The concentrations of activated sludge and GEM were still more than 2.80 g/L and 1.5 x 10(6)cells/mL, respectively, in the bioaugmented AnSBR. All the microbial communities changed indistinctively with time. The microbial community structures of the control AnSBR were similar to those of the bioaugmented one.

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.

Insights into the fate of a 13C labelled phenol pulse for stable isotope probing (SIP) experiments

Stable isotope probing (SIP) using DNA or RNA as a biomarker has proven to be a useful method for attributing substrate utilisation to specific microbial taxa. In this study we followed the transfer of a (13)C(6)-phenol pulse in an activated sludge micro-reactor to examine the resulting distribution of labelled carbon in the context of SIP. Most of the added phenol was metabolically converted within the first 100 min after (13)C(6)-phenol addition, with 49% incorporated into microbial biomass and 6% respired as CO(2). Less than 1% of the total (13)C labelled carbon supplied was incorporated into microbial RNA and DNA, with RNA labelling 6.5 times faster than DNA. The remainder of the added (13)C was adsorbed and/or complexed to suspended solids within the sludge. The (13)C content of nucleic acids increased beyond the initial consumption of the (13)C-phenol pulse. This study confirms that RNA labels more efficiently than DNA and reveals that only a small proportion of a pulse is incorporated into nucleic acids. Evidence of continued (13)C incorporation into nucleic acids suggests that cross-feeding of the SIP substrate was rapid. This highlights both the benefits of using a biomarker that is rapidly labelled and the importance of sampling within appropriate timescales to avoid or capture the effects of cross-feeding, depending on the goal of the study.

Influence of sustainability and immigration in assembling bacterial populations of known size and function

The rational assembly of microbial communities to perform desired functions would be of great practical benefit to society. Broadly speaking, there are two major theoretical foundations for microbial community assembly: one based on island biogeography theory and another based on niche theory. In this study, we compared a parameter from each theory (immigration rate and sustainability, respectively) to ascertain which was more influential in establishing a functional bacterial population in phenol degrading activated sludge over a 30-day period. Two bacterial strains originally isolated from activated sludge, but differing in their ability to sustain a population in this environment, were repeatedly added to activated sludge reactors at different doses. The resulting size of each population was monitored by competitive polymerase chain reaction. Large, unexpected, yet reproducible fluctuations in population sizes were observed. Irrespective of this, difference in the ability to sustain a population in this environment, overshadowed the influence of 100-fold differences in immigration rate.

PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites

tmoA and related genes encode the alpha-subunit of the hydroxylase component of the major group (subgroup 1 of subfamily 2) of bacterial multicomponent mono-oxygenase enzyme complexes involved in aerobic benzene, toluene, ethylbenzene and xylene (BTEX) degradation. A PCR-denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of tmoA-like gene sequences in environmental samples using a newly designed moderately degenerate primer set suitable for that purpose. In 35 BTEX-degrading bacterial strains isolated from a hydrocarbon polluted aquifer, tmoA-like genes were only detected in two o-xylene degraders and were identical to the touA gene of Pseudomonas stutzeri OX1. The diversity of tmoA-like genes was examined in DNA extracts from contaminated and non-contaminated subsurface samples at a site containing a BTEX-contaminated groundwater plume. Differences in DGGE patterns were observed between strongly contaminated, less contaminated and non-contaminated samples and between different depths, suggesting that the diversity of tmoA-like genes was determined by environmental conditions including the contamination level. Phylogenetic analysis of the protein sequences deduced from the amplified amplicons showed that the diversity of TmoA-analogues in the environment is larger than suggested from described TmoA-analogues from cultured isolates, which was translated in the DGGE patterns. Although different positions on the DGGE gel can correspond to closely related TmoA-proteins, relationships could be noticed between the position of tmoA-like amplicons in the DGGE profile and the phylogenetic position of the deduced protein sequence.

Bioaugmentation for bioremediation: the challenge of strain selection

Despite its long-term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ. These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information-based approach is already proving to be more effective than the traditional 'black-box' approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.

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.

Unique kinetic properties of phenol-degrading variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture

A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities. To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter(-1) day(-1)) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter(-1) day(-1) (enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a Variovorax ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus Variovorax and were shown to have high-affinity-type LmPHs. The LmPH of the Variovorax strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the Variovorax strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information, mechanisms accounting for the way the Variovorax population overgrew the chemostat enrichment are discussed.

Organization of the horizontally transferred pheBA operon and its adjacent genes in the genomes of eight indigenous Pseudomonas strains

Horizontal transfer of genes encoding phenol degradation (pheBA) in the environment has been previously described. Complete or partial phe-operon was redetected in plasmids of several indigenous Pseudomonas strains isolated from the river water. The sequences of up- and downstream regions of the acquired phe-DNA in eight different plasmids were analyzed. In all cases, miniature insertional elements or putative transposase genes were found suggesting transposase dependent pheBA integration into plasmids. In three cases, an open reading frame encoding homologue to the transcription regulator protein (CatR) of the pheBA operon was determined.

Molecular characterization of resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in petroleum-contaminated soil

PCR assays for analyzing resistance-nodulation-division transporters from solvent- and drug-resistant bacteria in soil were developed. Sequence analysis of amplicons showed that the PCR successfully retrieved transporter gene fragments from soil. Most of the genes retrieved from petroleum-contaminated soils formed a cluster (cluster PCS) that was distantly related to known transporter genes. Competitive PCR showed that the abundance of PCS genes is increased in petroleum-contaminated soil.

Comparing activated sludge and aerobic granules as microbial inocula for phenol biodegradation

Activated sludge and acetate-fed granules were used as microbial inocula to start up two sequencing batch reactors (R1, R2) for phenol biodegradation. The reactors were operated in 4-h cycles at a phenol loading of 1.8 kg m(-3) day(-1). The biomass in R1 failed to remove phenol and completely washed out after 4 days. R2 experienced initial difficulty in removing phenol, but the biomass acclimated quickly and effluent phenol concentrations declined to 0.3 mg l(-1) from day 3. The acetate-fed granules were covered with bacterial rods, but filamentous bacteria with sheaths, presumably to shield against toxicity, quickly emerged as the dominant morphotype upon phenol exposure. Bacterial adaptation to phenol also took the form of modifications in enzyme activity and increased production of extracellular polymers. 16S rRNA gene fingerprints revealed a slight decrease in bacterial diversity from day 0 to day 3 in R1, prior to process failure. In R2, a clear shift in community structure was observed as the seed evolved into phenol-degrading granules without losing species-richness. The results highlight the effectiveness of granules over activated sludge as seed for reactors treating toxic wastewaters.

Microbial diversity in biofilms from corroding heating systems

Culture-independent investigations of the bacterial diversity and activity in district heating systems with and without corrosion did not make it possible to relate one group of microorganisms with the observed corrosion. Fluorescence in situ hybridization by oligonucleotide probes revealed the dominance of beta-proteobacteria, sulphate reducing prokaryotes and alpha-proteobacteria. Analysis of a clone library from one Danish heating (DH) system showed that the most sequences formed two clusters within the alpha-proteobacteria affiliated to the families Rhizobiaceae and Acetobacteraceae and two clusters within the beta-proteobacteria belonging to the family Comamonadaceae. Functional groups were determined by microautoradiography showing aerobic and anaerobic bacteria (sulphate reducing and methanogenic bacteria). The corrosion study showed that pitting corrosion rates were five to ten times higher than the general corrosion rates, suggesting the presence of biocorrosion. The results indicate that several bacterial groups could be involved in corrosion of DH system piping including sulphate reducing prokaryotes, Acidovorax (within the beta-proteobacteria), methanogenic bacteria and others.

Temporal dynamics and degradation activity of an bacterial inoculum for treating waste metal-working fluid

In order for established bioreactors to be effective for treating chemically mixed wastes such as metal working fluids (MWF) it is essential that they harbour microbial populations that can maintain sufficient active biomass and degrade each of the chemical constituents present. In this study we investigated the effectiveness of a bacterial consortium composed of four species (Clavibacter michiganensis, Methylobacterium mesophilicum, Rhodococcus erythropolis and Pseudomonas putida), assembled on the basis of their apparent ubiquity in waste MWF, degradation ability and tolerance to fluctuating chemistry of the waste. The temporal dynamics of the inoculum and its effects on the fate of individual chemical components of the waste were studied, by regular sampling, over 400 h. Using a complementary approach of culture with chemotaxonomic (FAME) analysis and applying group specific probes (FISH), the inoculum was found to represent a significant component of the community in bioreactors with and without presence of indigenous MWF populations. In addition, the reduction in the COD by the consortium was approximately 85% of the total pollution load, and 30-40% more effectively than any other treatment (indigenous MWF community alone or activated sludge). Furthermore, all the chemical constituents, including the biocide (a formaldehyde release agent) demonstrated > 60% reduction. Many chemical components of the MWF proved to be recalcitrant in the other treatments. The results of this study confirm that assemblage of an inoculum, based on a comprehensive knowledge of the indigenous microbial community, in the target habitat, is a highly effective way of selecting microbial populations for bioaugmentation of bioreactors.

Molecular and physiological approaches to understanding the ecology of pollutant degradation

Pollutant biodegradation in the environment occurs in the context of various interactions among microorganisms. To understand this ecological process, identification of functionally important populations is considered to be the primary step, which can be followed by isolation and laboratory pure-culture studies of the important organisms. Laboratory studies can then proceed to the analysis of in situ activity and interactions with other organisms. Such studies will shape a deeper understanding of the ecology of pollutant degradation and facilitate the development of new bioremediation strategies.

Linking genetics, physiology and ecology: an interdisciplinary approach for advancing bioremediation

Our understanding of microbial catabolic pathways relevant to bioremediation has been shaped by laboratory studies using isolated pollutant-degrading microorganisms. Recent investigations of natural microbial communities have, however, suggested that catabolic populations in the environment are much more diverse than those previously isolated in the laboratory. In addition, most laboratory strains are now thought to constitute minor populations in the environment, sharing only small contributions to bioremediation processes. Currently, attempts to isolate microorganisms that constitute major populations in the environment have been initiated with the aid of molecular ecological techniques. Such studies will provide information more directly relevant to the catabolic reactions occurring in bioremediation processes and are thus expected to help develop new strategies for advancing bioremediation. This article outlines our studies on phenol-degrading bacteria in activated sludge to illustrate a possible scheme of how genetic and physiological information obtained in the laboratory can be applied to advancing bioremediation processes.