Genomic resolution of bacterial populations in saccharin and cyclamate degradation

The benefits of extensive artificial sweeteners use come at a cost of their ubiquitous occurrence in the aquatic environment. Biodegradation is crucial for the removal of artificial sweeteners in the environment, yet comprehensive characterizations of the degradation consortia that degrade these compounds have not been initiated. Here, we performed metagenomic analysis of microbial communities fulfilling complete mineralization of two typical artificial sweeteners, i.e. saccharin and cyclamate. Genome-resolved metagenomics enabled the recovery and metabolic characterization of total 23 population genomes from 8 phyla in the two consortia, most of which represented novel species. The saccharin-degrading consortia was notably dominated by a betaproteobacterial genome from the family Rhodocyclaceae, accounting for 15.5% of total sequences. For the cyclamate enrichment, 28.1% of the total sequences were assigned to three similarly abundant Alphaproteobacteria population genomes belonging to the family Sphingomonadaceae and Methylobacteriaceae. The metabolic potential of these population genomes were examined to potentially identify the roles of these populations in biodegradation of artificial sweeteners, and focusing on the energy and nutrient metabolisms.

Isolation and characterization of Sphingomonadaceae from fouled membranes

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42 oC, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling.

Sphingobium aromaticivastans sp. nov., a novel aniline- and benzene-degrading, and antimicrobial compound producing bacterium

A strictly aerobic, orange-pigmented strain was isolated and designated as UCM-25^T. This strain is capable of degrading aniline and benzene, while is also producing antimicrobial compounds which inhibit the growth of some common pathogenic microbes. A near full-length 16S rRNA gene sequence revealed similarity to Sphingobium chlorophenolicum NBRC 16172^T (98.6%). The level of DNA-DNA hybridization between the new isolate and the related species suggests UCM-25^T to be a new species belonging to the genus Sphingobium. The bacterial cells contained phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, three unidentified polar lipids, and an unidentified aminophospholipid. Ubiquinone Q-10 was the major quinone and spermidine was the major polyamine. The G+C content in the DNA of strain UCM-25^T was 62.9 mol%. Cells contained summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0, and C_14:0 2-OH as major fatty acids. Based on the comparison of phenotypic, genotypic, and chemotaxonomic characteristics, strain UCM-25^T represents a new member of the genus Sphingobium, for which the name S. aromaticivastans sp. nov. is proposed. The type strain is UCM-25^T (=KACC 19288^T =DSM 105181^T).

Further Understanding of Degradation Pathways of Microcystin-LR by an Indigenous Sphingopyxis sp. in Environmentally Relevant Pollution Concentrations

Microcystin-LR (MC-LR) is the most widely distributed microcystin (MC) that is hazardous to environmental safety and public health, due to high toxicity. Microbial degradation is regarded as an effective and environment-friendly method to remove it, however, the performance of MC-degrading bacteria in environmentally relevant pollution concentrations of MC-LR and the degradation pathways remain unclear. In this study, one autochthonous bacterium, Sphingopyxis sp. m6 which exhibited high MC-LR degradation ability, was isolated from Lake Taihu, and the degrading characteristics in environmentally relevant pollution concentrations were demonstrated. In addition, degradation products were identified by utilizing the full scan mode of UPLC-MS/MS. The data illustrated that strain m6 could decompose MC-LR (1–50 μg/L) completely within 4 h. The degradation rates were significantly affected by temperatures, pH and MC-LR concentrations. Moreover, except for the typical degradation products of MC-LR (linearized MC-LR, tetrapeptide, and Adda), there were 8 different products identified, namely, three tripeptides (Adda-Glu-Mdha, Glu-Mdha-Ala, and Leu-MeAsp-Arg), three dipeptides (Glu-Mdha, Mdha-Ala, and MeAsp-Arg) and two amino acids (Leu, and Arg). To our knowledge, this is the first report of Mdha-Ala, MeAsp-Arg, and Leu as MC-LR metabolites. This study expanded microbial degradation pathways of MC-LR, which lays a foundation for exploring degradation mechanisms and eliminating the pollution of microcystins (MCs).

Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy

Stable isotope probing (SIP) is a cultivation-independent approach identifying the functional microbes in their natural habitats, possibly linking their identities to functions. DNA-SIP is well-established but suffers from the shift of ¹²C-DNA into the heavy DNA (¹³C-DNA) fraction, which significantly reduces the resolution and accuracy. In this study, we coupled magnetic-nanoparticle mediated isolation (MMI) and DNA-SIP, namely MMI-SIP, to identify the active microbes involved in phenanthrene degradation from PAH-contaminated wastewater. Microbes affiliated to Pseudomonas and Sphingobium were responsible for in situ phenanthrene metabolism from the SIP results, and Pigmentiphaga was only unraveled for phenanthrene degradation in the MMI and MMI-SIP microcosms. MMI-SIP also significantly increased the enrichment of the above microbes and genes encoding the alpha subunit of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) in the heavy DNA fractions. Our findings suggest that MMI-SIP is a powerful tool, with higher resolution and accuracy, to distinguish the active microbes involved in phenanthrene metabolism in the wastewater, provide a more precise map of functional microbial communities, and offer suggestions for effective management for wastewater treatment plants.

Genomic and Proteomic Evidences for Exopolysaccharide Biosynthesis in Sphingobium chungbukense DJ77

Sphingobium chungbukense DJ77 is a Gram-negative bacterium has metabolic capability of producing exopolysaccharide (EPS) as a potential reducing and stabilizing agent for metallic nanoparticle synthesis. In this study, we investigated the genomic and proteomic analysis to verify metabolic pathway and involved genes and enzymes related to EPS biosynthesis in S. chungbukense DJ77. End-sequencing results of randomly selected fosmid library, which were prepared from high molecular weight DNA of S. chungbukense DJ77, showed identity to sequences from genes related the EPS biosynthesis pathways in several bacteria. We also observed that proteomic responses in S. chungbukense DJ77 by heterogeneously expressing gelA and gelN involved in gellan biosynthesis in Sphingomonas elodea. Comparative two-dimensional gel electrophoresis revealed that both GelA and GelN altered internal expression levels of proteins involved in EPS biosynthesis in S. chungbukense DJ77. The results might provide the genomic and proteomic evidences for presence of EPS biosynthesis pathways in S. chungbukense DJ77.

3,6-Dichlorosalicylate Catabolism Is Initiated by the DsmABC Cytochrome P450 Monooxygenase System in Rhizorhabdus dicambivorans Ndbn-20

The degradation of the herbicide dicamba is initiated by demethylation to form 3,6-dichlorosalicylate (3,6-DCSA) in Rhizorhabdusdicambivorans Ndbn-20. In the present study, a 3,6-DCSA degradation-deficient mutant, Ndbn-20m, was screened. A cluster, dsmR1DABCEFGR2, was lost in this mutant. The cluster consisted of nine genes, all of which were apparently induced by 3,6-DCSA. DsmA shared 30 to 36% identity with the monooxygenase components of reported three-component cytochrome P450 systems and formed a monophyletic branch in the phylogenetic tree. DsmB and DsmC were most closely related to the reported [2Fe-2S] ferredoxin and ferredoxin reductase, respectively. The disruption of dsmA in strain Ndbn-20 resulted in inactive 3,6-DCSA degradation. When dsmABC, but not dsmA alone, was introduced into mutant Ndbn-20m and Sphingobium quisquiliarum DC-2 (which is unable to degrade salicylate and its derivatives), they acquired the ability to hydroxylate 3,6-DCSA. Single-crystal X-ray diffraction demonstrated that the DsmABC-catalyzed hydroxylation occurred at the C-5 position of 3,6-DCSA, generating 3,6-dichlorogentisate (3,6-DCGA). In addition, DsmD shared 51% identity with GtdA (a gentisate and 3,6-DCGA 1,2-dioxygenase) from Sphingomonas sp. strain RW5. However, unlike GtdA, the purified DsmD catalyzed the cleavage of gentisate and 3-chlorogentisate but not 6-chlorogentisate or 3,6-DCGA in vitro Based on the bioinformatic analysis and gene function studies, a possible catabolic pathway of dicamba in R. dicambivorans Ndbn-20 was proposed.IMPORTANCE Dicamba is widely used to control a variety of broadleaf weeds and is a promising target herbicide for the engineering of herbicide-resistant crops. The catabolism of dicamba has thus received increasing attention. Bacteria mineralize dicamba initially via demethylation, generating 3,6-dichlorosalicylate. However, the catabolism of 3,6-dichlorosalicylate remains unknown. In this study, we cloned a gene cluster, dsmR1DABCEFGR2, involved in 3,6-dichlorosalicylate degradation from R. dicambivorans Ndbn-20, demonstrated that the cytochrome P450 monooxygenase system DsmABC was responsible for the 5-hydroxylation of 3,6-dichlorosalicylate, and proposed a dicamba catabolic pathway. This study provides a basis to elucidate the catabolism of dicamba and has benefits for the ecotoxicological study of dicamba. Furthermore, the hydroxylation of salicylate has been previously reported to be catalyzed by single-component flavoprotein or three-component Rieske non-heme iron oxygenase, whereas DsmABC was the only cytochrome P450 monooxygenase system hydroxylating salicylate and its methyl- or chloro-substituted derivatives.

Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer

Bacteria belonging to the genera Sphingomonas and Sphingobium are known for their ability to catabolize aromatic compounds. In this study, we analyzed the whole genome sequences of 26 strains in the genera Sphingomonas and Sphingobium to gain insight into dissemination of bioremediation capabilities, biodegradation potential, central pathways and genome plasticity. Phylogenetic analysis revealed that both Sphingomonas sp. strain BHC-A and Sphingomonas paucimobilis EPA505 should be placed in the genus Sphingobium. The bph and xyl gene cluster was found in 6 polycyclic aromatic hydrocarbons-degrading strains. Transposase and IS coding genes were found in the 6 gene clusters, suggesting the mobility of bph and xyl gene clusters. β-ketoadipate and homogentisate pathways were the main central pathways in Sphingomonas and Sphingobium strains. A large number of oxygenase coding genes were predicted in the 26 genomes, indicating a huge biodegradation potential of the Sphingomonas and Sphingobium strains. Horizontal gene transfer related genes and prophages were predicted in the analyzed strains, suggesting the ongoing evolution and shaping of the genomes. Analysis of the 26 genomes in this work contributes to the understanding of dispersion of bioremediation capabilities, bioremediation potential and genome plasticity in strains belonging to the genera Sphingomonas and Sphingobium.

Residues His172 and Lys238 are Essential for the Catalytic Activity of the Maleylacetate Reductase from Sphingobium chlorophenolicum Strain L-1

Maleylacetate reductase (PcpE), the last enzyme in the pentachlorophenol biodegradation pathway in Sphingobium chlorophenolicum L-1, catalyzes two consecutive reductive reactions, reductive dehalogenation of 2-chloromaleylacetate (2-CMA) to maleylacetate (MA) and subsequent reduction of MA to 3-oxoadipate (3-OXO). In each reaction, one molecule of NADH is consumed. To better understand its catalytic function, we undertook a structural model-based site-directed mutagenesis and steady-state kinetics study of PcpE. Our results showed that the putative catalytic site of PcpE is located in a positively charged solvent channel at the interface of the two domains and the binding of 2-CMA/MA involves seven basic amino acids, His172, His236, His237, His241 and His251, Lys140 and Lys238. Mutagenesis studies showed that His172 and Lys238 are essential for the catalytic activity of PcpE. However, the mutation of His236 to an alanine can increase the catalytic efficiency (k _cat /K _m ) of PcpE by more than 2-fold, implying that PcpE is still in an early stage of molecular evolution. Similar to tetrachlorobenzoquinone reductase (PcpD), PcpE is also inhibited by pentachlorophenol in a concentration-dependent manner. Furthermore, our studies showed that PcpE exhibits an extremely low but detectable level of alcohol dehalogenase activity toward ethanol and supports the notion that it is evolved from an iron-containing alcohol dehydrogenase.

Diversity and temporal shifts of the bacterial community associated with a toxic cyanobacterial bloom: An interplay between microcystin producers and degraders

The biodegradation of microcystins (MCs) by bacteria constitutes an important process in freshwater ecosystems to prevent the accumulation of toxins. However, little is known about the diversity and the seasonal dynamics of the bacterial community composition (BCC) involved in the degradation of MCs in nature. To explore these BCC shifts, high-throughput sequencing was used to analyse the 16S rRNA, mcyE and mlrA genes during a year in a freshwater reservoir with a toxic cyanobacterial bloom episode. The analysis of the mcyE and mlrA genes from water samples revealed the coexistence of different MC-producing and MC-degrading genotypes, respectively. The patchy temporal distribution of the mlrA genotypes (from the families Sphingomonadaceae and Xanthomonadaceae) suggests their dissimilar response to environmental conditions and the influence of other factors besides the MCs that may control their presence and relative abundance. During the maximum toxic cyanobacterial biomass and cell lysis, other bacterial taxa that lack mlr genes increased their relative abundance. Among these bacteria, those with a recognized role in the degradation of xenobiotic and other complex organic compounds (e.g., orders Myxococcales, Ellin6067, Spirobacillales and Cytophagales) were the most representative and suggest their possible involvement in the removal of MCs in the environment.

Heterologous expression of mlrA gene originated from Novosphingobium sp. THN1 to degrade microcystin-RR and identify the first step involved in degradation pathway

Information on the catalytic role of mlrA gene-encoded enzyme (MlrA) in microcystin-RR (MC-RR) biodegradation was limited. This study succeeded in expressing mlrA homolog of Novosphingobium sp. THN1 in heterologous host for the first time, by constructing a recombinant bacterium. Mass spectrometric analysis showed that the recombinant MlrA hydrolyzed MC-RR into linear intermediate product by cleaving the peptide bond between Adda and arginine residue, greatly detoxifying MC-RR. This finding clearly manifested that the MlrA homolog of THN1 strain possesses its original catalytic function, and ring-opening constituted the first step in MC-RR biodegradation pathway of THN1 strain. Moreover, MC-RR degradation by intact recombinant cells and cell-free crude enzyme (CE) from recombinant was compared. Results exhibited that intact recombinant was able to degrade 20 μg mL^-1 MC-RR more quickly than CE, with the maximum rate of 9.22 μg mL^-1 h^-1 in the first 8 h. Thus, this study provided new insights on the catalytic activity and roles of MlrA originated from THN1 strain in MC-RR biodegradation process, which lay a foundation for efficiently removing and detoxifying MC-RR, and exploring downstream steps in MC-RR biodegradation pathway of THN1 strain.

Evaluation of bacterial biodegradation and accumulation of phenanthrene in the presence of humic acid

This study evaluated the effect of humic acid (HA) on physicochemical properties of bacterial surfaces and on mass transfer of polycyclic aromatic hydrocarbons (PAHs) from aqueous phase into intracellular bacteria. Due to this process' potential for bacterial degradation, using Sphingobium sp. PHE3, degradation of phenanthrene (PHE) was compared in HA and non-HA sets. The results showed that approximately 51.1% of PHE at a concentration of 102.0 mg L^-1 was biodegraded in the non-HA sets, whereas almost all PHE was biodegraded with HA after 72 h. Interestingly, PHE that accumulated in the intracellular bacteria reached 3.80 mg L^-1 for the HA sets, which was significantly higher than that of non-HA. Lipid inclusion bodies appeared when Sphingobium sp. PHE3 was treated with HA. The results were further confirmed by the enhanced bacterial surface sorption capacity for the HA sets. Therefore, we concluded that added HA not only act as carriers and biosurfactants facilitating PHE uptake but also adjust bacteria cell wall properties for internalizing PHE, which ultimately overcame the PHE bioavailability resulting in enhanced biodegradation.

Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26

Bacterial evolution has resulted in the appearance of several Sphingomonadacea strains that gained the ability to metabolize hexachlorocyclohexanes (HCHs). HCHs have been widely used as pesticides but were banned under the Stockholm Convention on persistent organic pollutants (POPs) in 2009. Here we present evidence for bacterial transformation reactions of hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. HBCDs were used as flame retardants. They are now also considered as POPs and their production and use is restricted since 2013. Racemic α-, β-, and γ-HBCDs and their mixture were exposed to Sphingobium chinhatense IP26 in resting cell assays in parallel to β-HCH. All HBCD stereoisomers were converted with (-)β-HBCD being the best and both α-HBCD enantiomers the poorest substrates. HBCD conversion rates were 27-430 times slower than that of β-HCH. Three generations of hydroxylated transformation products were observed, 7 pentabromocyclododecanol isomers (PeBCD-ols), 11 tetrabromocyclododecadiols (TeBCD-diols) and 3 tribromocyclododecatriols (TrBCD-triols). The conversion of (+)α-, (-)β- and (-)γ-HBCD was faster than those of their enantiomers. Therefore the respective enantiomeric excess increased to 3 ± 1%, 36 ± 1% and 6 ± 2% during 48 h of bacterial exposure. PeBCD-ols appeared first, followed by TeBCD-diols and TrBCD-triols indicating stepwise hydrolytic dehalogenation reactions. In conclusion, severe HCH pollution at geographically distinct dumpsites triggered bacterial evolution to express enzymes transforming such compounds. We used S. chinhatense IP26 bacteria to transform structurally related HBCDs, also regulated under the Stockholm Convention. Such bacteria might be useful for bioremediation but the toxicity of the numerous transformation products observed must be assessed in advance.

Genome Organization of Sphingobium indicum B90A: An Archetypal Hexachlorocyclohexane (HCH) Degrading Genotype

Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during γ-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment.

Effects of dissolved organic matter derived from forest leaf litter on biodegradation of phenanthrene in aqueous phase

Dissolved organic matter (DOM) released from forest leaf litter is potentially effective for the degradation of polycyclic aromatic hydrocarbons (PAHs), yet the inherent mechanism remains insufficiently elucidated. In this study, we investigated the effects of DOM derived from Pinus elliottii and Schima superba leaf litter on the degradation of phenanthrene by the phenanthrene degrading bacterium Sphingobium sp. Phe-1. DOM from different origins and at a large range of concentrations enhanced the degradation rate of phenanthrene. DOM derived from P. elliottii leaf litter decomposed for 12 months used at a concentration of 100mg/L yielded the highest degradation rate (16.9% in 36h) and shortened the degradation time from 48h to 24h. Changes in the composition of DOM during degradation as measured by EEMs-FRI showed that proteins and tyrosine in the DOM supplied readily available nutrients that stimulated biological activity of Phe-1, increasing its growth rate and catechol 2,3-dioxygenase activity. Simultaneously, fulvic acid and humic acid in the DOM enhanced phenanthrene bioavailability by increasing the solubility and mass transfer of phenanthrene, enhancing the uptake kinetics of Phe-1, and increasing the bacteria's direct access to DOM-associated phenanthrene. Humic acid was co-metabolized by Phe-1, resulting in further stimulation of phenanthrene degradation.

Physiological and Transcriptome Response of the Polycyclic Aromatic Hydrocarbon Degrading Novosphingobium sp. LH128 after Inoculation in Soil

Soil bioaugmentation involves the inoculation of pollutant-degrading bacteria to accelerate pollutant degradation. Often the inoculum shows a dramatic decrease in Colony Forming Units (CFU) upon soil inoculation but this behavior is not well-understood. In this study, the physiology and transcriptomic response of a GFP tagged variant of Novosphingobium sp. LH128 was examined after inoculation into phenanthrene spiked soil. Four hours after inoculation, strain LH128-GFP showed about 99% reduction in CFU while microscopic counts of GFP-expressing cells were identical to the expected initial cell density, indicating that the reduction in CFU number is explained by cells entering into a Viable But Non-Culturable (VBNC)-like state and not by cell death. Transcriptome analysis showed a remarkably higher expression of phenanthrene degradation genes 4 h after inoculation, compared to the inoculum suspension concomitant with an increased expression of genes involved in stress response. This indicates that the cells were active in phenanthrene degradation while experiencing stress. Between 4 h and 10 days, CFU numbers increased to numbers comparable to the inoculated cell density. Our results suggest that strain LH128-GFP enters a VBNC-like state upon inoculation into soil but is metabolically active and that VBNC cells should be taken into account in evaluating bioaugmentation approaches.

Soil-Bacterium Compatibility Model as a Decision-Making Tool for Soil Bioremediation

Bioremediation of organic pollutant contaminated soil involving bioaugmentation with dedicated bacteria specialized in degrading the pollutant is suggested as a green and economically sound alternative to physico-chemical treatment. However, intrinsic soil characteristics impact the success of bioaugmentation. The feasibility of using partial least-squares regression (PLSR) to predict the success of bioaugmentation in contaminated soil based on the intrinsic physico-chemical soil characteristics and, hence, to improve the success of bioaugmentation, was examined. As a proof of principle, PLSR was used to build soil-bacterium compatibility models to predict the bioaugmentation success of the phenanthrene-degrading Novosphingobium sp. LH128. The survival and biodegradation activity of strain LH128 were measured in 20 soils and correlated with the soil characteristics. PLSR was able to predict the strain's survival using 12 variables or less while the PAH-degrading activity of strain LH128 in soils that show survival was predicted using 9 variables. A three-step approach using the developed soil-bacterium compatibility models is proposed as a decision making tool and first estimation to select compatible soils and organisms and increase the chance of success of bioaugmentation.

Cyanotoxin degradation activity and mlr gene expression profiles of a Sphingopyxis sp. isolated from Lake Champlain, Canada

A bacterium capable of degrading five microcystin (MC) variants, microcystin-LR, YR, LY, LW and LF at an initial total concentration of 50 μg l^-1 in less than 16 hours was isolated from Missisquoi Bay, in the south of Quebec, Canada. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Sphingopyxis sp., designated strain MB-E. It was shown that microcystin biodegradation activity was reduced at acidic and basic pH values. Even though no biodegradation occurred at pH values of 5.05 and 10.23, strain MB-E was able to degrade MCLR and MCYR at pH 9.12 and all five MCs variants tested at pH 6.1. Genomic sequencing revealed that strain MB-E contained the microcystin degrading gene cluster, including the mlrA, mlrB, mlrC and mlrD genes, and transcriptomic analysis demonstrated that all of these genes were induced during the degradation of MCLR alone or in the mixture of all five MCs. This novel transcriptomic analysis showed that the expression of the mlr gene cluster was similar for MCLR alone, or the mixture of MCs, and appeared to be related to the total concentration of substrate. The results suggested that the bacterium used the same pathway for the degradation of all MC variants.

Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments

At the same time that the European Union (EU) policy recommend to direct efforts towards reductions of heavy metals, polycyclic aromatic hydrocarbons (PAHs) and mining residues, there is the need to increase the cultivable areas within Europe to cope with the increasing demands for food and energy crops. Bioremediation is a good technique for the restoration of contaminated soils; however, it has not been used extensively because of the variability of the outcome. This variability is frequently due to a bad establishment of foreign degrading populations in soil. We have demonstrated that Novosphingobium sp. HS2aR (i) is able to compete with other root colonizers and with indigenous bacteria, (ii) is able to establish in high numbers in the contaminated environments and (iii) is able to remove more than 90 % of the extractable phenanthrene in artificially contaminated soils. Furthermore, we have demonstrated that the capacity to remove phenanthrene is linked to the ability to promote plant growth in contaminated environments. The fact that the presence of Novosphingobium sp. HS2aR improves the growth of plants in contaminated soil suggests that it may be a useful strain for utilization in amelioration of soil quality while improving the growth of economically important energy crops, thus adding value to the bioremediation strategy.

Enhanced Biological Trace Organic Contaminant Removal: A Lab-Scale Demonstration with Bisphenol A-Degrading Bacteria Sphingobium sp. BiD32

Discharge of trace organic contaminants (TOrCs) from wastewater treatment plants (WWTPs) may contribute to deleterious effects on aquatic life. Release to the environment occurs both through WWTP effluent discharge and runoff following land applications of biosolids. This study introduces Enhanced Biological TOrC Removal (EBTCR), which involves continuous bioaugmentation of TOrC-degrading bacteria for improved removal in WWTPs. Influence of bioaugmentation on enhanced degradation was investigated in two lab-scale sequencing batch reactors (SBRs), using bisphenol A (BPA) as the TOrC. The reactors were operated with 8 cycles per day and at two solids retention times (SRTs). Once each day, the test reactor was bioaugmented with Sphingobium sp. BiD32, a documented BPA-degrading culture. After bioaugmentation, BPA degradation (including both the dissolved and sorbed fractions) was 2-4 times higher in the test reactor than in a control reactor. Improved removal persisted for >5 cycles following bioaugmentation. By the last cycle of the day, enhanced BPA removal was lost, although it returned with the next bioaugmentation. A net loss of Sphingobium sp. BiD32 was observed in the reactors, supporting the original hypothesis that continuous bioaugmentation (rather than single-dose bioaugmentation) would be required to improve TOrCs removal during wastewater treatment. This study represents a first demonstration of a biologically based approach for enhanced TOrCs removal that both reduces concentrations in wastewater effluent and prevents transfer to biosolids.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Pathway for Biodegrading Nodularin (NOD) by Sphingopyxis sp. USTB-05

Nodularin (NOD) is greatly produced by Nodularia spumigena and released into the environment when toxic cyanobacterial blooms happened in natural water body, which is seriously harmful to human and animals. The promising bacterial strain of Sphingopyxis sp. USTB-05 was found to have an ability in biodegrading NOD. Initially, 11.6 mg/L of NOD could be completely eliminated within 72 h by whole cells of USTB-05, and within 36 h by its crude enzymes (CEs) of 570 mg/L, respectively. During the enzymatic biodegradation process of NOD, two products were observed on the profiles of HPLC. Based on the analysis of m/z ratios of NOD and its two products on a rapid-resolution liquid chromatogram-mass spectrum (RRLC-MS), we suggested that at least two enzymes of USTB-05 participated in biodegrading NOD. The first enzyme hydrolyzed Arg-Adda peptide bond of cyclic NOD and converted it to linear NOD as the first product. The second enzyme was found to cut off the target peptide bond between Adda and Glu of linearized NOD, and Adda was produced as a second and dead-end product. This finding is very important in both basic research and the application of USTB-05 on the removal of NOD from a water environment.

Proteomics of Sphingobium indicum B90A for a deeper understanding of hexachlorocyclohexane (HCH) bioremediation

Genome wide expression profiling of Sphingobium indicum B90A revealed induction of lin genes, linA and linB, involved in dechlorination of hexachlorocyclohexane (HCH), in the presence of all four isomers of HCH. Supporting proteomics data, the qPCR and promoter assay showed upregulation of linA transcription in the presence of HCH isomers. Analysis of the upstream region of the linA gene revealed the existence of the GntR binding site overlapping the -10 hexamer of the putative promoter motif. As GntR is a known transcription repressor its dissociation from the linA promoter is expected to induce lin genes in the presence of HCH isomers. Comparison of in situ and in-culture proteomics indicated expression lin genes at the dumpsite, an indication for the in situ HCH degradation.

Bioremediation potential of a highly mercury resistant bacterial strain Sphingobium SA2 isolated from contaminated soil

A mercury resistant bacterial strain, SA2, was isolated from soil contaminated with mercury. The 16S rRNA gene sequence of this isolate showed 99% sequence similarity to the genera Sphingobium and Sphingomonas of α-proteobacteria group. However, the isolate formed a distinct phyletic line with the genus Sphingobium suggesting the strain belongs to Sphingobium sp. Toxicity studies indicated resistance to high levels of mercury with estimated EC50 values 4.5 mg L(-1) and 44.15 mg L(-1) and MIC values 5.1 mg L(-1) and 48.48 mg L(-1) in minimal and rich media, respectively. The strain SA2 was able to volatilize mercury by producing mercuric reductase enzyme which makes it potential candidate for remediating mercury. ICP-QQQ-MS analysis of Hg supplemented culture solutions confirmed that almost 79% mercury in the culture suspension was volatilized in 6 h. A very small amount of mercury was observed to accumulate in cell pellets which was also evident according to ESEM-EDX analysis. The mercuric reductase gene merA was amplified and sequenced. The deduced amino acid sequence demonstrated sequence homology with α-proteobacteria and Ascomycota group.

Cooperative Mn(II) oxidation between two bacterial strains in an aquatic environment

In natural or engineered environments, diverse interspecific interactions among two or more microbial taxa may profoundly affect the transformation of organic compounds in the media. Little is known, however, about how these organisms and interactions affect the transformation of heavy metals. Recently, we found an interaction between two non-Mn(II)-oxidizing (when in monoculture) strains, Arthrobacter sp. QXT-31 and Sphingopyxis sp. QXT-31, which, when cultured in combination, resulted in Mn(II)-oxidizing activity in synthetic media. In order to study the occurrence likelihood of cooperative Mn(II) oxidation in natural water and discharged effluent, we initially identified an optimal ratio of the two strains in a combined culture, as well as the impacts of external factors on the cooperative oxidation. Once preferred initial conditions were established, we assessed the degree and rate of Mn(II) oxidation mediated by the combined QXT-31 strains (henceforth referred to as simply 'QXT-31') in three different water types: groundwater, domestic sewage and coking wastewater. Results showed that Mn(II) oxidation only occurred when the two strains were within a specific ratios range. When introduced to the test waters at the preferred ratio, QXT-31 demonstrated high Mn(II)-oxidizing activities, even when relative abundance of QXT-31 was very low (roughly 1.6%, calculated by 454 pyrosequencing events on 16S rcDNA). Interestingly, even under low relative abundance of QXT-31, removal of total organic carbon and total nitrogen in the test waters was significantly higher than the control treatments that were not inoculated with QXT-31. Data from our study indicate that cooperative Mn(II) oxidation is most likely to occur in natural aquatic ecosystems, and also suggests an alternative method to treat wastewater containing high concentrations of Mn(II).