The degradation of alkylphenols by Sphingomonas sp. strain TTNP3 – a review on seven years of research

Complete biodegradation of tetrabromobisphenol A through sequential anaerobic reductive dehalogenation and aerobic oxidation

Tetrabromobisphenol A (TBBPA), a common brominated flame retardant and a notorious pollutant in anaerobic environments, resists aerobic degradation but can undergo reductive dehalogenation to produce bisphenol A (BPA), an endocrine disruptor. Conversely, BPA is resistant to anaerobic biodegradation but susceptible to aerobic degradation. Microbial degradation of TBBPA via anoxic/oxic processes is scarcely documented. We established an anaerobic microcosm for TBBPA dehalogenation to BPA facilitated by humin. Dehalobacter species increased with a growth yield of 1.5 × 108 cells per μmol Br- released, suggesting their role in TBBPA dehalogenation. We innovatively achieved complete and sustainable biodegradation of TBBPA in sand/soil columns columns, synergizing TBBPA reductive dehalogenation by anaerobic functional microbiota and BPA aerobic oxidation by Sphingomonas sp. strain TTNP3. Over 42 days, 95.11 % of the injected TBBPA in three batches was debrominated to BPA. Following injection of strain TTNP3 cells, 85.57 % of BPA was aerobically degraded. Aerobic BPA degradation column experiments also indicated that aeration and cell colonization significantly increased degradation rates. This treatment strategy provides valuable technical insights for complete TBBPA biodegradation and analogous contaminants.

The Changes of Phyllosphere Fungal Communities among Three Different Populus spp

As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves' physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely-P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves' chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.

Long-Chain Alkylphenol Biodegradation Potential of Soil Ascomycota

A total of 11 ascomycete strains destructing technical nonylphenol (NP) and 4-tert-octylphenol (4-t-OP) were isolated from NP-contaminated soddy-podzolic loamy soil (Leningrad Region, Russia). The isolates proved capable of degrading NP and 4-t-OP at a high load (300 mg/L). The most efficient Fusarium solani strain 8F degraded alkylphenols (APs) both in cometabolic conditions and in the absence of additional carbon and energy sources. A decrease in APs was due to biodegradation or biotransformation by the strain and, to a minor extent, absorption by fungal cells. NP and 4-t-OP half-lives were, respectively, 3.5 and 6.4 h in cometabolic conditions and 9 and 19.7 h in the absence of additional carbon and energy sources. Amounts of the lipid peroxidation product malondialdehyde (MDA) and reduced glutathione (GSH) increased during NP and 4-t-OP biodegradation in cometabolic conditions by 1.7 and 2 times, respectively, as compared with a control. A high GSH level in F. solani 8F cells potentially implicated the metabolite in both AP biodegradation and strain resistance to oxidative stress. The study is the first to report on the NP and 4-t-OP degradation by the ascomycete F. solani in cometabolic conditions and in the absence of additional carbon and energy sources. The high AP degradation potential of soil ascomycetes was assumed to provide a basis for new environmentally safe bioremediation technologies for purification of soils and natural and waste waters contaminated with endocrine disruptors.

Novel nonylphenol-degrading bacterial strains isolated from sewage sludge: Application in bioremediation of sludge

Nonylphenol (NP) is an anthropogenic pollutant frequently found in sewage sludge due to the insufficient degrading effectiveness of conventional WWTPs and has attracted attention as an endocrine disruptor. The aim of this study was to isolate specific NP-degrading bacteria from sewage sludge to be used in the degradation of this contaminant through bioaugmentation processes in aqueous solution and sewage sludge. Up to eight different bacterial strains were isolated, six of them not previously described as NP degraders. Bacillus safensis CN12 presented the best NP degradation in solution, and glucose used as an external carbon source increased its effect, reaching DT₅₀ degradation values (time to decline to half the initial concentration of the pollutant) of only 0.9 days and a complete degradation in <7 days. Four NP metabolites were identified throughout the biodegradation process, showing higher toxicity than the parent contaminant. In sewage sludge suspensions, the endogenous microbiota was capable of partially degrading NP, but a part remained adsorbed as bound residue. Bioaugmentation was used for the first time to remove NP from sewage sludge to obtain more environmentally friendly biosolids. However, B. safensis CN12 was not able to degrade NP due to its high adsorption on sludge, but the use of a cyclodextrin (HPBCD) as availability enhancer allowed us to extract NP and degrade it in solution. The addition of glucose as an external carbon source gave the best results since the metabolism of the sludge microbiota was activated, and HPBCD was able to remove NP from sewage sludge to the solution to be degraded by B. safensis CN12. These results indicate that B. safensis CN12 can be used to degrade NP in water and sewage sludge, but the method must be improved using consortia of B. safensis CN12 with other bacterial strains able to degrade the toxic metabolites produced.

Quantitative proteomic analysis reveals the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 in the process of simultaneous nitrogen and phenol removal

Phenol and ammonia in wastewater pose a serious threat to ecosystems and human health. However, the currently limited studies on single bacterium simultaneously removing phenol and nitrogen pollution have not fully elucidated the relevant metabolic mechanisms. The differences in proteomic profile after supplementing with phenol and ammonia for 6 and 24 h, respectively, were evaluated to explore the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 during the simultaneous removal process of phenol and nitrogen. Results revealed that a new potential phenol para-degradation pathway appeared in T2. Phenol induced changes in nitrogen metabolism, resulting in increased denitrification and decreased synthesis of glutamate from ammonia at 6 h. In addition, phenol exposure enhanced the expression of cytochrome oxidases with high oxygen affinity and increased ATP synthesis. The increase in chemotaxis and flagellar assembly was conducive to the uptake and utilization of phenol. The synthesis of lipoic acid and biotin was also promoted to resist phenol toxicity. Moreover, phenol triggered cellular stress response, thereby leading to the upregulation of anti-stress proteins, such as universal stress protein, iron‑sulfur cluster protein, and chaperones. This study contributes to revealing the metabolic characteristics and adaptive mechanism of T2 during simultaneous nitrogen and phenol removal. SIGNIFICANCE: Phenol and ammonia often co-exist in wastewater, causing serious environmental problems. The information on the metabolic mechanism of simultaneously removing these two pollutants by bacteria is insufficient at present. Moreover, phenol is toxic to microbial and causes cells damage. Therefore, exploring the response mechanism of bacteria to phenol stress is conducive to understand their tolerance mechanism to aromatic compounds. In this study, the metabolic characteristics and adaptive mechanism of C. oxalaticus T2 during the simultaneous removal of phenol and nitrogen process were evaluated by comparing the proteome profiles at different stages. The results revealed the degradation pathways of phenol and nitrogen by strain T2. A variety of phenol response mechanisms were determined, including enhanced energy production, improved cell motility, increased the synthesis of lipoic acid and biotin, and combined action of multiple anti-stress proteins. This study is potentially useful to future phenol and nitrogen co-pollution bioremediation strategies and provides insight into the phenolic compound resistance mechanism in bacteria.

Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability

The increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic offshore samples. We recovered 48 novel metagenome-assembled genomes. Metagenomic recruitment revealed a significant change in the microbial community which was dominated by several Proteobacteria orders (Sphingomonadales, Pseudomonadales, Caudobacterales and Rhizobiales). Genomic potential for bioremediation processes, including nitrate removal through aerobic denitrification, and degradation of aromatic compounds and other toxic products were enriched in these microbes. The detrimental side effects were the increased number of antimicrobial resistance genes and the presence of potentially emergent pathogens. Knowledge of this metabolic diversity and the microbes involved in ecological balance recovery can be used to reduce the environmental impact of these practices.

TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation

TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane.

Microbial transformation of widely used pharmaceutical and personal care product compounds

Pharmaceutical and personal care products (PPCPs) are commonly used chemicals that are increasingly detected in urban-impacted environments, particularly those receiving treated wastewater. PPCPs may have toxicological effects on the macrofauna that are exposed through contaminated water; thus, there is interest in microbially mediated transformations that may degrade PPCPs. This review discusses specific examples of PPCP transformations that may occur in anoxic environments, including O-methylation and O-demethylation.

Evolution of microbial community during dry storage and recovery of aerobic granular sludge

Aerobic granular sludge (AGS) was imbedded in agar and stored at 4 °C for 30 days, and then the stored granules were recovered in a sequencing batch reactor fed real wastewater within 11 days. Variations in microbial community compositions were investigated during dry storage and recovery of AGS, aiming to elucidate the mechanism of granular stability loss and recovery. The storage and recovery of AGS involved microbial community evolution. The dominant bacterial genera of the mature AGS were Zoogloea (relative abundance of 22.39%), Thauera (16.03%) and Clostridium_sensu_stricto (11.17%), and those of the stored granules were Acidovorax (26.79%), Macellibacteroides (12.83%) and Pseudoxanthomonas (5.69%), respectively. However, the dominant genera were Streptococcus (43.64%), Clostridium_sensu_stricto (12.3.6%) and Lactococcus (11.47%) in the recovered AGS. Methanogens were always the dominant archaeal species in mature AGS (93.01%), stored granules (99.99%) and the recovered AGS (94.84%). Facultative anaerobes and anaerobes proliferated and dominated in the stored granules, and their metabolic activities gradually led to granular structure destruction and property deterioration. However, the stored granules served as carriers for the microbes originated from the real septic tank wastewater during recovery. They proliferated rapidly and secreted a large number of extracellular polymeric substances which helped to recover the granular structure in 11 days.

Descriptive Bacterial and Fungal Characterization of Propolis Using Ultra-High-Throughput Marker Gene Sequencing

Bees harbor microorganisms that are important for host health, physiology, and survival. Propolis helps modulate the immune system and health of the colony, but little information is available about its microbial constituents. Total genomic DNA from samples of natural propolis from Apis mellifera production hives from four locations in Mexico were used to amplify a region of the 16S rRNA gene (bacteria) and the internal transcriber spacer (fungi), using PCR. The Illumina MiSeq platform was used to sequence PCR amplicons. Extensive variation in microbial composition was observed between the propolis samples. The most abundant bacterial group was Rhodopila spp. (median: 14%; range: 0.1%–27%), a group with one of the highest redox potential in the microbial world. Other high abundant groups include Corynebacterium spp. (median: 8.4%; 1.6%–19.5%) and Sphingomonas spp. (median: 5.9%; 0.03%–14.3%), a group that has been used for numerous biotechnological applications because of its biodegradative capabilities. Bacillus and Prevotella spp. alone comprised as much as 88% (53% and 35%, respectively) of all bacterial microbiota in one sample. Candida (2%–43%), Acremonium (0.03%–25.2%), and Aspergillus (0.1%–43%) were among the most abundant fungi. The results contribute to a better understanding of the factors associated with the health of Apis mellifera production hives.

Oxidative phase I metabolism of the UV absorber 2-(2H-benzotriazol-2-yl)-4,6-di-tert-pentylphenol (UV 328) in an in vitro model with human liver microsomes

2-(2H-Benzotriazol-2-yl)-4,6-di-tert-pentylphenol (UV 328, CAS: 25973-55-1) is an ultraviolet light (UV) absorber which is used as an additive for plastics and other polymeric substances to prevent the host material from light induced degradation reactions. However, no information about human exposure, metabolism and kinetics is available for this substance so far. Therefore, in vitro experiments with human liver microsomes were performed to derive oxidative phase I metabolites of UV 328 in an explorative approach using liquid-chromatography coupled with tandem mass spectrometry. Initially, a suspect screening mode was applied to the incubated samples. Six metabolites with hydroxy or oxo groups as well as a metabolite carrying both hydroxy and carbonyl moieties at the alkyl side chains were postulated and custom synthesized as reference standards. Afterwards, the results were verified in a target screening approach. Thereby, five of the six investigated analyte structures were confirmed. Quantitative estimations of the generated transformation products revealed 2-(2H-benzotriazol-2-yl)-6-(3-hydroxy-2-methylbutan-2-yl)-4-(tert-pentyl)phenol (UV 328-6/3-OH), 2-(2H-benzotriazol-2-yl)-4-(3-hydroxy-2-methylbutan-2-yl)-6-(tert-pentyl)phenol (UV 328-4/3-OH) and 2-(2H-benzotriazol-2-yl)-4-(2-methylbutan-3-on-2-yl)-6-(3-hydroxy-2-methylbutan-2-yl)phenol (UV 328-4/3-CO-6/3-OH) as most promising parameters. In summary, oxidation of both alkyl side chains at the phenol moiety was proven, but no metabolic transformations at the benzotriazole moiety were observed.

Comparative Analysis of the Genetic Basis of Branched Nonylphenol Degradation by Sphingobium amiense DSM 16289T and Sphingobium cloacae JCM 10874T

Branched nonylphenol (BNP), a degradation product of nonylphenol polyethoxylates, exerts estrogenic effects on various organisms. The genes underlying BNP degradation by Sphingobium amiense DSM 16289^T were analyzed by complete genome sequencing and compared with those of the versatile BNP-degrading Sphingobium cloacae JCM 10874^T. An opdA homolog (opdA_DSM16289) encoding BNP degradation activity was identified in DSM 16289^T, in contrast with JCM 10874^T, possessing both the opdA homolog and nmoA. The degradation profile of different BNP isomers was examined by Escherichia coli transformants harboring opdA_DSM16289, opdA_JCM10874, and nmoA_JCM10874 to characterize and compare the expression activities of these genes.

Biodegradation of 7-Hydroxycoumarin in Pseudomonas mandelii 7HK4 via ipso-Hydroxylation of 3-(2,4-Dihydroxyphenyl)-propionic Acid

A gene cluster, denoted as hcdABC, required for the degradation of 3-(2,4-dihydroxyphenyl)-propionic acid has been cloned from 7-hydroxycoumarin-degrading Pseudomonas mandelii 7HK4 (DSM 107615), and sequenced. Bioinformatic analysis shows that the operon hcdABC encodes a flavin-binding hydroxylase (HcdA), an extradiol dioxygenase (HcdB), and a putative hydroxymuconic semialdehyde hydrolase (HcdC). The analysis of the recombinant HcdA activity in vitro confirms that this enzyme belongs to the group of ipso-hydroxylases. The activity of the proteins HcdB and HcdC has been analyzed by using recombinant Escherichia coli cells. Identification of intermediate metabolites allowed us to confirm the predicted enzyme functions and to reconstruct the catabolic pathway of 3-(2,4-dihydroxyphenyl)-propionic acid. HcdA catalyzes the conversion of 3-(2,4-dihydroxyphenyl)-propionic acid to 3-(2,3,5-trihydroxyphenyl)-propionic acid through an ipso-hydroxylation followed by an internal (1,2-C,C)-shift of the alkyl moiety. Then, in the presence of HcdB, a subsequent oxidative meta-cleavage of the aromatic ring occurs, resulting in the corresponding linear product (2E,4E)-2,4-dihydroxy-6-oxonona-2,4-dienedioic acid. Here, we describe a Pseudomonas mandelii strain 7HK4 capable of degrading 7-hydroxycoumarin via 3-(2,4-dihydroxyphenyl)-propionic acid pathway.

Water contamination by endocrine disruptors: Impacts, microbiological aspects and trends for environmental protection

Hormone active agents constitute a dangerous class of pollutants. Among them, those agents that mimic the action of estrogens on target cells and are part of the group of endocrine-disruptor compounds (EDCs) are termed estrogenic EDCs, the main focus of this review. Exposure to these compounds causes a number of negative effects, including breast cancer, infertility and animal hermaphroditism. However, especially in underdeveloped countries, limited efforts have been made to warn people about this serious issue, explain the methods of minimizing exposure, and develop feasible and efficient mitigation strategies at different levels and in various environments. For instance, the use of bioremediation processes capable of transforming EDCs into environmentally friendly compounds has been little explored. A wide diversity of estrogen-degrading microorganisms could be used to develop such technologies, which include bioremediation processes for EDCs that could be implemented in biological filters for the post-treatment of wastewater effluent. This review describes problems associated with EDCs, primarily estrogenic EDCs, including exposure as well as the present status of understanding and the effects of natural and synthetic hormones and estrogenic EDCs on living organisms. We also describe potential biotechnological strategies for EDC biodegradation, and suggest novel treatment approaches for minimizing the persistence of EDCs in the environment.

Aerobic degradation of estrogenic alkylphenols by yeasts isolated from a sewage treatment plant

Long-chain alkylphenols including octylphenol (OP) are well-known toxic pollutants prevailing in the environment due to the massive demand of these chemicals in industry and have been identified as endocrine disrupting chemicals (EDCs).

Degradation and toxicity reduction of the endocrine disruptors nonylphenol, 4-tert-octylphenol and 4-cumylphenol by the non-ligninolytic fungus Umbelopsis isabellina

Nonylphenol (NP), 4-tert-octylphenol (4-t-OP) and 4-cumylphenol (4-CP) are pollutants that are known as endocrine disruptors mainly due to their estrogen-mimicking activity. These phenolic substances are used in a wide range of industrial and commercial applications. In the present study, biodegradation of tNP, 4-t-OP and 4-CP using the non-ligninolytic fungus Umbelopsis isabellina was investigated. After 12h of incubation, more than 90% of initially applied tNP, 4-t-OP and 4-CP (25mgL(-1)) were eliminated. GC-MS analysis revealed several derivatives mainly (hydroxyalkyl)phenols. Moreover, xenobiotic biotransformation led to the formation of intermediates with less harmful effects than the parent compounds. For all xenobiotics, a decrease in growth medium toxicity was observed, using Artemia franciscana and Daphnia magna as bioindicators. The results indicate that U. isabellina has potential in the degradation and detoxification of contaminants with endocrine activity. Moreover, this is the first report demonstrating that a microorganism is capable of effective 4-CP elimination.

Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants

Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.

Isomer-specific biodegradation of nonylphenol in an activated sludge bioreactor and structure-biodegradability relationship

Nonylphenol (NP), one of the priority hazardous substances, is in fact a mixture of numerous isomers. It is inconclusive whether or not biodegradation during wastewater treatment process is isomer-specific, leading to the environmental release of NP in different isomer profiles. In this study, we evaluated the isomer selectivity of 19 NP isomers in a laboratory-scale continuous flow conventional activated sludge bioreactor under various operational conditions. The removal efficiency of NP isomers ranged from 90 to 99%, depending on the operational conditions and isomer structures. Isomer selective biodegradation resulted in the increase of composition of recalcitrant isomers, such as, NP₁₉₃a/b, NP₁₁₀a and NP₁₉₄ in the effluent. Moreover, biodegradability was related to the bulkiness of α-substituents and followed α-dimethyl > α-ethyl-α-methyl > α-methyl-α-n-propyl > α-iso-propyl-α-methyl. Steric effect index, a quantitative descriptor of steric hindrance, was linearly correlated with residues of NP isomers in the effluent (R² = 0.76). Decrease of temperature to 10 °C decreased the overall biodegradability and also enhanced the relative enrichment of recalcitrant isomers. These findings suggest that isomer compositions of NP entering the environment may be different from those in technical mixtures and that isomeric selectivity should be taken into account to better understand the occurrence, fate, and ecological risks of NP.

Analysis, toxicity, occurrence and biodegradation of nonylphenol isomers: a review

Over the last two decades, nonylphenols (NPs) have become to be known as a priority hazardous substance due primarily to its estrogenicity and ubiquitous occurrence in the environment. Nonylphenols are commonly treated as a single compound in the evaluation of their environmental occurrence, fate and transport, treatment or toxicity. However, technical nonylphenols (tNPs) are in fact a mixture of more than 100 isomers and congeners. Recent studies showed that some of these isomers behaved significantly differently in occurrence, estrogenicity and biodegradability. The most estrogenic isomer was about 2 to 4 times more active than tNP. Moreover, the half lives of the most recalcitrant isomers were about 3 to 4 times as long as those of readily-biodegradable isomers. Negligence of NP's isomer specificity may result in inaccurate assessment of its ecological and health effects. In this review, we summarized the recent publications on the analysis, occurrence, toxicity and biodegradation of NP at the isomer level and highlighted future research needs to improve our understanding of isomer-specificity of NP.

Biodegradation and utilization of 4-n-nonylphenol by Aspergillus versicolor as a sole carbon and energy source

4-n-Nonylphenol (4-n-NP) is an environmental pollutant with endocrine-disrupting activities that is formed during the degradation of nonylphenol polyethoxylates, which are widely used as surfactants. Utilization of 4-n-NP by the filamentous fungus Aspergillus versicolor as the sole carbon and energy source was investigated. By means of gas chromatography-mass spectrometry, we showed that in the absence of any carbon source other than 4-n-NP in the medium, A. versicolor completely removed the xenobiotic (100 mg L(-1)) after 3 d of cultivation. Moreover, mass spectrometric analysis of intracellular extracts led to the identification of eight intermediates. The mineralization of the xenobiotic in cultures supplemented with 4-n-NP [ring-(14)C(U)] as a growth substrate was also assessed. After 3 d of incubation, approximately 50% of the initially applied radioactivity was recovered in the form of (14)CO2, proving that this xenobiotic was completely metabolized and utilized by A. versicolor as a carbon source. Based on microscopic analysis, A. versicolor is capable of germinating spores under such conditions. To confirm these observations, a microcalorimetric method was used. The results show that even the highest amount of 4-n-NP initiates heat production in the fungal samples, proving that metabolic processes were affected by the use of 4-n-NP as an energetic substrate.

Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment

The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.

Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern

Background

Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.

Results

PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.

Conclusions

In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.

Emerging chemicals and the evolution of biodegradation capacities and pathways in bacteria

The number of new chemicals produced is increasing daily by the thousands, and it is inevitable that many of these chemicals will reach the environment. Current research provides an understanding of how the evolution of promiscuous enzymes and the recruitment of enzymes available from the metagenome allows for the assembly of these pathways. Nevertheless, physicochemical constraints including bioavailability, bioaccessibility, and the structural variations of similar chemicals limit the evolution of biodegradation pathways. Similarly, physiological constraints related to kinetics and substrate utilization at low concentrations likewise limit chemical-enzyme interactions and consequently evolution. Considering these new data, the biodegradation decalogue still proves valid while at the same time the underlying mechanisms are better understood.