Structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics

Simultaneous high molecular weight PAHs degradation and chromate and arsenite detoxification by Altererythrobacter sp. H2

The cooccurrence of high molecular weight PAHs and heavy metals Cr and As is frequently observed in soil and water and challenges public health and environmental management. Yet the limited microbial resources were reported to simultaneously detoxify PAHs, Cr(VI) and As(III), which restricts the bioremediation of co-contaminated soil by PAHs, Cr and As. Here, we isolated Altererythrobacter sp. H2 and found it could degrade various PAHs, including phenanthrene, fluoranthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene, and tolerate and detoxify high concentrations of Cr(VI) and As(III). Genomic, transcriptomic, and biochemical assays reveal strain H2 degrades PAHs, reduces Cr(VI), and oxidize As(III) via a horizontally transferred RHO gene cluster, a chromate reductase ChrR, and a arsenite resistance gene cluster arsRBC. The horizontally transferred PAHs-degrading gene cluster encodes the Rieske dioxygenase three-component system and other enzymes required for PAHs degradation, which suggested those heavy metal-detoxifying bacteria could be excellent PAHs-degrading and heavy metal-detoxifying agents after accommodating a PAHs degradation gene cluster like strain H2 did. To our knowledge, strain H2 is the only reported Altererythrobacter member that uses a classical Rieske dioxygenase three-component system to initial PAHs degradation and the only one could simultaneously detoxify PAHs, Cr(VI), and As(III). Our study provides insights into the PAHs degradation mechanism of Altererythrobacter members and demonstrates the excellent potential of H2 in the bioremediation of both PAHs and heavy metal pollutants.

Hydroxyl radicals dominated the reduction of antibiotic resistance genes by inactivating Gram-negative bacteria during soil electrokinetic treatment

Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants that widely exist in the environment. Effective reduction of ARB and ARGs from soil and water could be achieved by electrokinetic remediation (EKR) technology. In water, hydroxyl radicals (·OH) are proved to play a major role in the EKR process; while the reduction mechanism of ARB and ARGs is still unclear in soil. In this study, different concentrations of hydroxyl radical scavengers (salicylic acid) were added to the EKR system to explore the possible role of ·OH in the reduction of ARB and ARGs. The results showed that generally, ·OH played a more vital role in the reduction of ARB (65.24-72.46%) compared to the reduction of total cultivable bacteria (57.50%). And ·OH contributed to a higher reduction of sul genes (60.94%) compared to tet genes (47.71%) and integrons (36.02%). It was found that the abundance of Gram-negative bacteria (Chloroflexi, Acidobacteria and norank_c_Acidobacteria) was significantly reduced, and the correlation between norank_f_Gemmatimonadaceae and sul1 was weakened in the presence of ·OH. Correlation analysis indicated that the abundance of ARGs (especially sul1) was closely related to the Gram-negative bacteria (Proteobacteria, Acidobacteria, and Gemmatimonadetes) in the soil EKR treatment. Moreover, changes in bacterial community structure affected the abundance of ARB and ARGs indirectly. Overall, this study revealed the reduction mechanism of ARB and ARGs by ·OH in the soil EKR system for the first time. These findings provide valuable support for soil remediation efforts focusing on controlling antibiotic resistance.

Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review

A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.

Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii

Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.

Diversity of Microbial Communities, PAHs, and Metals in Road and Leaf Dust of Functional Zones of Moscow and Murmansk

The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and leaf dust in three urban zones of Murmansk and Moscow with contrasting anthropogenic load were conducted. We found that the structure of bacterial communities affected the functional zoning of the city, biotope type, and geographical components. Fungal communities were instead impacted only by biotope type. Our findings revealed that the structure of fungal communities was mostly impacted by PAHs whereas bacterial communities were sensitive to metals. Bacteria of the genus Sphingomonas in road and leaf dust as indicators of the ecological state of the urban ecosystems were proposed.

Multi-Omic Profiling of a Newly Isolated Oxy-PAH Degrading Specialist from PAH-Contaminated Soil Reveals Bacterial Mechanisms to Mitigate the Risk Posed by Polar Transformation Products

Polar biotransformation products have been identified as causative agents for the eventual increase in genotoxicity observed after the bioremediation of PAH-contaminated soils. Their further biodegradation has been described under certain biostimulation conditions; however, the underlying microorganisms and mechanisms remain to be elucidated. 9,10-Anthraquinone (ANTQ), a transformation product from anthracene (ANT), is the most commonly detected oxygenated PAH (oxy-PAH) in contaminated soils. Sand-in-liquid microcosms inoculated with creosote-contaminated soil revealed the existence of a specialized ANTQ degrading community, and Sphingobium sp. AntQ-1 was isolated for its ability to grow on this oxy-PAH. Combining the metabolomic, genomic, and transcriptomic analyses of strain AntQ-1, we comprehensively reconstructed the ANTQ biodegradation pathway. Novel mechanisms for polyaromatic compound degradation were revealed, involving the cleavage of the central ring catalyzed by Baeyer-Villiger monooxygenases (BVMO). Abundance of strain AntQ-1 16S rRNA and its BVMO genes in the sand-in-liquid microcosms correlated with maximum ANTQ biodegradation rates, supporting the environmental relevance of this mechanism. Our results demonstrate the existence of highly specialized microbial communities in contaminated soils responsible for processing oxy-PAHs accumulated by primary degraders. Also, they underscore the key role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of PAH-contaminated soils.

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

Assessments of Bacterial Community Shifts in Sediments along the Headwaters of São Francisco River, Brazil

Sustainable use of freshwater resources for human civilization needs requires the assessment and monitoring of freshwater health, and bacterial communities from riverbed sediments have been shown to be susceptible to chronic anthropogenic disturbances in freshwater ecosystems. Here, we took advantage of the occurrence of well-recognized adjacent sections from the Upper São Francisco River basin with well-recognized levels of anthropogenic activity intensity to test the applicability of sediment bacterial communities as bioindicators of impacts on freshwater ecosystems. We applied 16S amplicon sequencing to estimate the diversity and composition of bacterial communities from 12 sampling sites across the Upper São Francisco River basin, classified as being of no, low, or high intensity of anthropogenic activities, and used diversity metrics and LEfSe to compare the patterns of community structure. Our results revealed that accessed sediment environments associated with land areas with a high intensity of anthropogenic activities presented the lowest levels of community diversity, and the bacterial community compositions of these environments were significantly different from the other sampled areas. Our findings can be considered a source of evidence for the usefulness of bacterial community-based approaches as a tool for diagnosis and monitoring of ecosystem health in areas of vulnerable freshwater environments, and can even be incorporated into regular water quality programs.

Impact of long-term industrial contamination on the bacterial communities in urban river sediments

BACKGROUND

The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.

RESULTS

The overall community composition and abundance of individual bacterial groups differed between samples. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P < 0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.

CONCLUSIONS

Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

Interactions between elevated CO2 levels and floating aquatic plants on the alteration of bacterial function in carbon assimilation and decomposition in eutrophic waters

Elevated atmospheric CO₂ concentration (eCO₂) may have different effects on the bacterial community with regard to C assimilation and decomposition in eutrophic waters compared to that in fresh waters with intermediate levels of nutrients and oceans. Aquatic plant growth under eCO₂ could further modify microbial activities associated with the C cycle in eutrophic waters. Therefore, there is an urgent need to further study how eCO₂ and its interactions with the growth of aquatic plants affect the composition and function of the bacterial community involved in mediating the C cycle in eutrophic waters. Accordingly, we designed a microcosm experiment to investigate the effects of ambient and high CO₂ concentrations on bacterial community composition and function in eutrophic waters with and without the growth of Eichhornia crassipes (Mart.) Solms. The results from 16S rRNA gene sequencing, function prediction, and q-PCR showed that eCO₂ significantly increased the abundance of bacterial and functional genes involved in CO₂ assimilation (photosynthetic bacteria; cbbL IA & IC, cbbL ID, cbbM, pufM) and C decomposition (Acidimicrobiia, Thermoleophilia, Gaiellales; ChiA), illustrating the functional enrichment with photoautotrophy, hydrocarbon degradation, cellulolysis, and aromatic hydrocarbon degradation. However, eCO₂ decreased the abundance of some chemoautotrophic bacteria, including nitrifying bacteria (Nitrospirae, Nitrosomonadaceae). In contrast, the cultivation of E. crassipes decreased the abundance of photosynthetic bacteria but increased the abundance of bacteria involved in complex C decomposition associated with root exudates and degradation, e.g. Fibrobacteres, Sphingobacteriales, Sphingomonadales, and Rhizobiales. eCO₂ and growth of E. crassipes had opposite effects on algal density in eutrophic waters, creating interactive effects that further decreased the diversity of the bacterial community and abundance of some CO₂-assimilating bacteria with nitrifying characteristics (Nitrosomonadaceae) and some C-degrading bacteria (Fibrobacteres) with denitrifying properties (Flavobacteriaceae, Sphingomonadaceae, and Gemmobacter). Therefore, the interactions between aquatic plants and the bacterial community in eutrophic waters under eCO₂ would be beneficial to the environment and help alleviate the greenhouse effect.

A new framework for approaching precision bioremediation of PAH contaminated soils

Bioremediation is a sustainable treatment strategy which remains challenging to implement especially in heterogeneous environments such as soil and sediment. Herein, we present a novel precision bioremediation framework that integrates amplicon based metagenomic analysis and chemical profiling. We applied this approach to samples obtained at a site contaminated with polycyclic aromatic hydrocarbons (PAHs). Geobacter spp. were identified as biostimulation targets because they were one of the most abundant genera and previously identified to carry relevant degradative genes. Mycobacterium and Sphingomonads spp. were identified as bioaugmentation and genetic bioaugmentation targets, respectively, due to their positive associations with PAHs and their high abundance and species diversity at all sampling locations. Overall, this case study suggests this framework can help identify bacterial targets for precision bioremediation. However, it is imperative that we continue to build our databases as the power of metagenomic based approaches remains limited to microorganisms currently in our databases.

Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil

BACKGROUND

Studying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil).

RESULTS

Analysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides.

CONCLUSION

Altogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.

Flourishing deep-sea AAP bacteria detected by flow cytometric sorting and molecular analysis

Pigmented bacteria cells, including aerobic anoxygenic phototrophic (AAP) bacteria, contribute significantly to secondary production and aquatic carbon cycling but their distribution in the deep sea is still not well understood, especially in the South China Sea. In this study, microscopic, flow cytometric, and molecular analyses were carried out to investigate the abundance and diversity of AAP bacteria at seven stations in the South China Sea. The results revealed the existence of bacteriochlorophyll-containing bacteria below 500 m from two of seven stations. Flow cytometric analysis detected red and infra-red fluorescence under blue (488 nm) light excitation from fluorescent cells. Blue light-excited red fluorescence of these cells from the 1000 m depth at station E403 were verified using epifluorescence microscopy. Based on fluorescence and side scatter features, fluorescent cells were sorted and subjected to molecular analysis. DNA was extracted from these sorted cells from both stations for PCR amplification using 16S rDNA primers. Sequencing of the PCR products showed that the sorted cells from the 1000 m depth at station E403 belonged to the genus Porphyrobacter. The cell population sorted from 500 m at station E703 contained Sphingomonas and a Methylobacterium-like taxon. All these three taxa belong to aerobic anoxygenic phototrophic alpha-proteobacteria. Using flow cytometric analysis, we found that the abundance of Porphyrobacter sp. at 1000 m was 2.71–2.95×10⁴ cells mL^-1 whereas cell counts of Sphingomonas sp. and Methylobacterium at 500 m were about 3.75–4.12×10⁵ cells mL^-1. These results indicate that albeit not ubiquitous in deep water, bacteriochlorophyll-containing bacteria can be abundant in the deep-sea aphotic zone.

Pre-coagulation coupled with sponge-membrane filtration for organic matter removal and membrane fouling control during drinking water treatment

A new hybrid system was developed in this study for the treatment of drinking water consisting of pre-coagulation using polyaluminium chloride (PACl) and membrane filtration (MF) with sponge cubes acting as biomass carriers (P-SMF). When compared to a conventional MF (CMF) and a MF after coagulation by utilizing PACl (P-MF), better removal of nutrients, UV₂₅₄ and dissolved organic carbon (DOC) (>65%) was obtained from the P-SMF. The accumulation of biopolymers (including polysaccharides and proteins), humic substances, hydrophilic organics, and other small molecular weight (MW) organic matter in the CMF led to the most severe membrane fouling coupled with the highest pore blocking and cake resistance. Pre-coagulation was ineffective in eliminating small MW and hydrophilic organic matter. Conversely, the larger MW organics (i.e. biopolymers and humic substances), small MW organics and hydrophilic organic compounds could be removed in significantly larger quantities in the P-SMF by PACl coagulation. This was achieved via adsorption and the biodegradation by attached biomass on these sponges and by the suspended sludge. Further analyses of the microbial community indicated that the combined addition of PACl and sponges generated a high enrichment of Zoolgloea, Amaricoccus and Reyranella leading to the reduction of biopolymers, and Flexibacter and Sphingobium were linked to the degradation of humic substances. Moreover, some members of Alphaproteobacteria in the P-SMF may be responsible for the removal of low MW organics. These results suggest that the pre-coagulation process coupled with adding sponge in the MF system is a promising technology for mitigating membrane fouling.

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Sediment bacterial communities play a critical role in biogeochemical cycling in lotic ecosystems. Despite their ecological significance, the effects of urban discharge on spatiotemporal distribution of bacterial communities are understudied. In this study, we examined the effect of urban discharge on the spatiotemporal distribution of stream sediment bacteria in a northeast Ohio stream. Water and sediment samples were collected after large storm events (discharge > 100 m) from sites along a highly impacted stream (Tinkers Creek, Cuyahoga River watershed, Ohio, USA) and two reference streams. Although alpha (α) diversity was relatively constant spatially, multivariate analysis of bacterial community 16S rDNA profiles revealed significant spatial and temporal effects on beta (β) diversity and community composition and identified a number of significant correlative abiotic parameters. Clustering of upstream and reference sites from downstream sites of Tinkers Creek combined with the dominant families observed in specific locales suggests that environmentally-induced species sorting had a strong impact on the composition of sediment bacterial communities. Distinct groupings of bacterial families that are often associated with nutrient pollution (i.e., Comamonadaceae, Rhodobacteraceae, and Pirellulaceae) and other contaminants (i.e., Sphingomonadaceae and Phyllobacteriaceae) were more prominent at sites experiencing higher degrees of discharge associated with urbanization. Additionally, there were marked seasonal changes in community composition, with individual taxa exhibiting different seasonal abundance patterns. However, spatiotemporal variation in stream conditions did not affect bacterial community functional profiles. Together, these results suggest that local environmental drivers and niche filtering from discharge events associated with urbanization shape the bacterial community structure. However, dispersal limitations and interactions among other species likely play a role as well.

Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs

Novosphingobium sp. HR1a is able to grow using diverse polycyclic aromatic hydrocarbons (PAHs) as the sole carbon sources. We have identified two transposons that contain genes encoding several ring-hydroxylating dioxygenases and we have demonstrated the crucial role of one of these dioxygenases in the PAH metabolism in this strain; a mutant in the large subunit of this dioxygenase was unable to growth with 2-, 3-, or 4-rings aromatic hydrocarbons. Using a construction of lacZ gene fused with the pathway promoter, we determined that the expression of the dioxygenase gene was specifically induced in the presence of some PAHs and intermediates of their metabolic pathway. In silico analysis of the ORFs within the transposons and construction of the corresponding knock-out mutants allowed us to identify the main regulatory protein involved in PAH degradation in Novosphingobium sp. HR1a. To our knowledge this is the first time that a regulatory protein controlling the degradation pathway of high-molecular weight PAHs has been investigated. A deeper knowledge of the regulatory circuits that control the expression of PAH degradation has allowed us to design two biosensors for monitoring environments contaminated with oil-derived mixtures. Novosphingobium sp. HR1a (pKSR-1), the biosensor based on the promoter of the regulatory protein PahR, was more sensitive and faster in the detection of aromatic contaminants in environmental samples than Novosphingobium sp. HR1a (pKSA-1), the biosensor that is based on the PAHs-dioxygenase promoter (P_pahA). Novosphingobium sp. HR1a (pKSR-1) was able to detect PAHs in the range of μgl^-1 (ppb).

Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions

Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene’s function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Plasmid-Mediated Tolerance Toward Environmental Pollutants

The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils

The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively.

Polycyclic aromatic hydrocarbons in deep sea sediments: Microbe-pollutant interactions in a remote environment

Recalcitrant polycyclic aromatic hydrocarbons (PAHs) released into seawater end up in the deep sea sediments (DSSs). However, their fate here is often oversimplified by theoretical models. Biodegradation of PAHs in DSSs, is assumed to be similar to biodegradation in surface habitats, despite high hydrostatic pressures and low temperatures that should significantly limit PAH biodegradation. Bacteria residing in the DSSs (related mainly to α- and γ-Proteobacteria) have been shown to or predicted to possess distinct genes, enzymes and metabolic pathways, indicating an adaptation of these bacterial communities to the psychro-peizophilic conditions of the DSSs. This work summarizes some of the most recent research on DSS hydrocarbonoclastic populations and mechanisms of PAH degradation and discusses the challenges posed by future high CO2 and UV climate scenarios on biodegradation of PAHs in DSSs.

Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family

Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.

Genotypic diversity and antibiotic resistance in Sphingomonadaceae isolated from hospital tap water

The aim of this study was to infer about the modes and extent of dispersion of Sphingomonadaceae via tap water. Sphingomonadaceae isolated from tap water samples in different places of a hospital were compared, based on intra-species genetic variability and antibiotic resistance phenotypes. These isolates were also compared with others isolated before from houses and dental chairs, served by the same municipal water supply system. Sphingomonadaceae from hospital tap water comprised members of the genera Sphingomonas, Sphingobium, Novosphingobium and Blastomonas. In general, distinct genotypes of Sphingomonadaceae were detected in different hospital areas and in tap water outside the hospital, suggesting these bacteria are not persistent or widespread in the urban water distribution system. Possible intrinsic antibiotic resistance, observed in most or all members of the family or of a genus, was observed for colistin in Sphingomonadaceae, aminoglycosides in the genus Blastomonas and beta-lactams in the genus Sphingobium. Possible acquired resistance phenotypes, not common to all members of a given species, comprised fluoroquinolones, cephalosporins and sulphonamides. Although the potential of Sphingomonadaceae as opportunistic pathogens may be low, the capacity of these bacteria to thrive in water supply systems, combined with the intrinsic or acquired antibiotic resistance, may raise the risk associated with their occurrence in hospital tap water.

Abilities and genes for PAH biodegradation of bacteria isolated from mangrove sediments from the central of Thailand

PAH-degrading bacteria, including Novosphingobium sp. PCY, Microbacterium sp. BPW, Ralstonia sp. BPH, Alcaligenes sp. SSK1B, and Achromobacter sp. SSK4, were isolated from mangrove sediments. These isolates degraded 50-76% of 100 mg/l phenanthrene within 2 weeks. Strains PCY and BPW also degraded pyrene at 98% and 71%, respectively. Furthermore, all of them probably produced biosurfactants in the presence of hydrocarbons. Interestingly, PCY has a versatility to degrade various PAHs. Molecular techniques and plasmid curing remarkably revealed the presence of the alpha subunit of pyrene dioxygenase gene (nidA), involving in its pyrene/phenanthrene degrading ability, located on megaplasmid of PCY which has never before been reported in sphingomonads. Moreover, genes encoding ferredoxin, reductase, extradiol dioxygenase (bphA3A4C) and exopolysaccharide biosynthetase, which may be involved in PAH degradation and biosurfactant production, were also found in PCY. Therefore, we conclude that these isolates, especially PCY, can be the candidates for use as inoculums in the bioremediation.

Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium

A Gram-negative, aerobic, copper-resistant bacterium, designated strain CU4T, was isolated from copper mine soil in Daye, China. Phylogenetic analysis based on 16S rRNA gene sequences showed highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.4 %), followed by Sphingobium francense Sp+T (97.2 %), Sphingobium japonicum UT26T (97.1 %), Sphingobium abikonense NBRC 16140T (97.0 %), Sphingobium xenophagum DSM 6383T (96.9 %) and Sphingobium yanoikuyae DSM 7462T (95.5 %). The major fatty acids (>5 %) were summed feature 7 (C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), summed feature 4 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH, and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylcholine. The genomic DNA G+C content of strain CU4T was 64.9 mol%. Comparison of DNA–DNA hybridization, phenotypic and chemotaxonomic characteristics between strain CU4T and phylogenetically related strains revealed that the new isolate represents a novel species of the genus Sphingobium , for which the name Sphingobium cupriresistens sp. nov. is proposed. The type strain is CU4T ( = KCTC 23865T = CCTCC AB 2011146T). An emended description of the genus Sphingobium is also proposed.

Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124(T), was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124(T) grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124(T) showed highest 16S rRNA gene sequence similarity to Novosphingobium barchaimii LL02(T) (98.5%), Novosphingobium panipatense SM16(T) (98.1%), Novosphingobium soli CC-TPE-1(T) (97.9%), Novosphingobium naphthalenivorans TUT562(T) (97.6%), Novosphingobium mathurense SM117(T) (97.5%) and Novosphingobium resinovorum NCIMB 8767(T) (97.5%) and lower sequence similarity (<97%) to all other members of the genus Novosphingobium. The DNA-DNA relatedness between strain LE124(T) and N. barchaimii LL02(T) and other related type strains was found to vary from 15% to 45% confirming that it represents a novel species. The genomic DNA G+C content of strain LE124(T) was 60.7 mol%. The predominant fatty acids were summed feature 8 (C18:1ω7c, 49.1%), summed feature 3 (C16:1ω7c/C16:1ω6c, 19.9%), C16:0 (6.7%), C17:1ω6c (4.9%) and a few hydroxyl fatty acids, C14:0 2-OH (9.4%) and C16:0 2-OH (2.1%). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA-DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124(T) represents a novel species within the genus Novosphingobium for which we propose the name Novosphingbium lindaniclasticum sp. nov. The type strain is LE124(T) (=CCM 7976(T)=DSM 25409(T)).

Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585(T), was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585(T) was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis. Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T). The polar lipids of strain G1A_585(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585(T) was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585(T) ( = DSM 25081(T)  = LMG 26646(T)). Because Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T) form a phylogenetic group together with strain G1A_585(T) that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151(T) = DSM 16223(T) = KCTC 12232(T)), Sphingorhabdus marina comb. nov. (type strain FR1087(T) = DSM 22363(T) = IMSNU 14132(T) = KCTC 12763(T) = JCM 14161(T)) and Sphingorhabdus litoris comb. nov. (type strain FR1093(T) = DSM 22379(T) = IMSNU 14133(T) = KCTC 12764(T) = JCM 14162(T)).

Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, designated F2(T), was isolated from an HCH dumpsite at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Sphingobium. Its closest neighbour was Sphingobium japonicum UT26(T) (99.2% 16S rRNA gene sequence similarity). The DNA G+C content was 65.7 mol%. The polyamine profile showed the presence of spermidine. The respiratory pigment was ubiquinone Q-10. The predominant cellular fatty acids were C(16:0) (12.5%), C(14:0) 2-OH (8.1%), summed feature 3 (consisting of C(16:1)ω7c and/or C(16:1)ω6c; 5.8%) and summed feature 8 (consisting of C(18:1)ω7c and/or C(18:1)ω6c; 53.1%). The major polar lipids of strain F2(T) were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. DNA-DNA relatedness and biochemical and physiological characters clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain F2(T) represents a novel species of the genus Sphingobium, for which the name Sphingobium lucknowense sp. nov. is proposed. The type strain is strain F2(T) (=MTCC 9456(T) =CCM 7544(T)).

Changes in pelagic bacteria communities due to leaf litter addition

In many limnetic systems, the input of allochthonous organic matter, e.g., leaf litter, is a substantial source of dissolved organic carbon (DOC) for pelagic bacteria, especially in fall and winter when autochthonous DOC production is low. However, relatively little is known about community changes of pelagic lake bacteria due to leaf litter input which includes both the release of leaf leachates and microorganisms from the leaf litter into the surrounding water. Therefore, we have experimentally studied the effects of different types of leaf litter (Betula pendula, Fagus silvatica, and Pinus silvestris) on the pelagic bacterial community composition by adding leaves to different treatments of epilimnic water samples (unfiltered, 0.2 µm and 5.0 µm-pre-filtered) from humic Lake Grosse Fuchskuhle (Northeastern Germany). The addition of leaf litter led to a significant increase in DOC concentration in lake water, and each leaf litter type produced significantly different amounts of DOC (p = <0.001) as well as of specific DOC fractions (p = <0.001), except of polysaccharides. DGGE banding patterns varied over time, between types of leaf litter, and among treatments. Bacteria belonging to known bacterial phylotypes in the southwest basin of Lake Grosse Fuchskuhle were frequently found and even persisted after leaf litter additions. Upon leaf litter addition, α-proteobacteria (Azospirillum, Novosphingobium, and Sphingopyxis) as well as β-proteobacteria (Curvibacter and Polynucleobacter) were enriched. Our results indicate that supply of leaf litter DOM shifted the bacterial community in the surrounding water towards specific phylotypes including species capable of assimilating the more recalcitrant DOC pools. Statistical analyses, however, show that DGGE banding patterns are not only affected by DOC pools but also by treatment. This indicates that biological factors such as source community and grazing may be also important for shifts in bacterial community structure following leaf litter input into different lakes.

Enrichment and cultivation of pelagic bacteria from a humic lake using phenol and humic matter additions

Individual bacterial populations are known to respond differently toward substrate availability. To test how the availability of either pure phenol or natural humic matter (HM) selects for specific pelagic bacteria phylotypes from a humic lake (Lake Grosse Fuchskuhle, northeastern Germany), we used culture-dependent and -independent approaches. Using a batch approach, the bacterial community composition (BCC) differed depending on both the quantity and the quality of added substrates. Using a dilution-to-extinction approach, distinct BCC were detected by eliminating less abundant species. Most bacteria that were common in the lake were favored by phenol, and yet different subsets of the native BCC were enriched by HM. Specific bacterial groups with different growth requirements were consistently present, negatively influenced, or positively enriched following substrate additions. This study comprises the first explicit demonstration that bacteria such as Methylobacterium, Methylophilus, and Methylosinus spp. can be enriched on phenol or HM. Our isolation approaches led to the successful cultivation of a variety of native bacteria from the lake, such as Novosphingobium (Alphaproteobacteria) and Flexibacter (Bacteroidetes), or phenol-utilizing bacteria such as members of Actinobacteria or Burkholderia (Betaproteobacteria). Enrichment and cultivation on phenol and HM as substrates revealed highly specialized bacterial communities that resemble those found in many HM-rich lakes.

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment.

Horizontal gene transfer in metal and radionuclide contaminated soils

The horizontal transfer of genes encoded on mobile genetic elements (MGEs) such as plasmids and phage and their associated hitchhiking elements (transposons, integrons, integrative and conjugative elements, and insertion sequences) rapidly accelerate genome diversification of microorganisms, thereby affecting their physiology, metabolism, pathogenicity,and ecological character. The analyses of completed prokaryotic genomes reveal that horizontal gene transfer (HGT) continues to be an important factor contributing to the innovation of microbial genomes. Indeed, microbial genomes are remarkably dynamic and a considerable amount of genetic information is inserted or deleted by HGT mechanisms. Thus, HGT and the vast pool of MGEs provide microbial communities with an unparalleled means by which to respond rapidly to changing environmental conditions and exploit new ecological niches. Metals and radionuclide contamination in soils, the subsurface, and aquifers poses a serious challenge to microbial growth and survival because these contaminants cannot be transformed or biodegraded into non-toxic forms as often occurs with organic xenobiotic contaminants. In this chapter we present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contributions of HGT to adaptation for survival in mixed waste sites.

Molecular characteristics of xenobiotic-degrading sphingomonads

The genus Sphingomonas (sensu latu) belongs to the alpha-Proteobacteria and comprises strictly aerobic chemoheterotrophic bacteria that are widespread in various aquatic and terrestrial environments. The members of this genus are often isolated and studied because of their ability to degrade recalcitrant natural and anthropogenic compounds, such as (substituted) biphenyl(s) and naphthalene(s), fluorene, (substituted) phenanthrene(s), pyrene, (chlorinated) diphenylether(s), (chlorinated) furan(s), (chlorinated) dibenzo-p-dioxin(s), carbazole, estradiol, polyethylene glycols, chlorinated phenols, nonylphenols, and different herbicides and pesticides. The metabolic versatility of these organisms suggests that they have evolved mechanisms to adapt quicker and/or more efficiently to the degradation of novel compounds in the environment than members of other bacterial genera. Comparative analyses demonstrate that sphingomonads generally use similar degradative pathways as other groups of microorganisms but deviate from competing microorganisms by the existence of multiple hydroxylating oxygenases and the conservation of specific gene clusters. Furthermore, there is increasing evidence for the existence of plasmids that only can be disseminated among sphingomonads and which undergo after conjugative transfer pronounced rearrangements.

Microbial biodegradation of polyaromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.

Distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26

Sphingobium japonicum (formerly Sphingomonas paucimobilis) UT26 utilizes the important insecticide gamma-hexachlorocyclohexane as a sole source of carbon and energy. In previous studies, we isolated and characterized six structural genes (linA to linF) and one regulatory gene (linR) of UT26 for the degradation of gamma-hexachlorocyclohexane to beta-ketoadipate. Our analysis in this study indicated that the UT26 genome consists of three large circular replicons of 3.6 Mb, 670 kb, and 185 kb. The 3.6 Mb and the 670 kb replicons had one and two copies, respectively, of the 16S ribosomal RNA gene, and these replicons were designated as chromosomes (Chr) I and II, respectively. Chr I was indicated to be a main chromosome carrying the dnaA gene. The first three lin genes, linA to linC, for conversion of gamma-hexachlorocyclohexane to 2,5-dichlorohydroquinone, were dispersed on Chr I. The 185 kb plasmid, pCHQ1, carried the linRED operon for the conversion of 2,5-dichlorohydroquinone to maleylacetate and was conjugatively transferred to another sphingomonad strain. The linF gene encoding maleylacetate reductase was located on Chr II. These results indicated that the genes for the complete gamma-hexachlorocyclohexane degradation are dispersed on the three large replicons of UT26.

Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads

Sphingopyxis terrae, and Sphingopyxis macrogoltabida strains 103 and 203, can degrade polyethylene glycols (PEGs). They differ in the following respects: (i) different substrate specificities (chain length) of assimilable PEG, (ii) PEG-inducible or constitutive PEG-degradative proteins, and (iii) symbiotic or axenic degradation of PEG. S. terrae was able to incorporate PEG 6000, but strain 103 could not incorporate more than PEG 4000, suggesting that the difference in assimilable PEG chain length depends on the ability to take up substrate. PEG-degradative genes (pegB, C, D, A, E and R) from these strains were cloned. Their primary structures shared a high homology of more than 99 %. The peg genes encode a TonB-dependent receptor (pegB), a PEG-aldehyde dehydrogenase (pegC), a permease (pegD), a PEG dehydrogenase (pegA) and an acyl-CoA ligase (pegE), and in the opposite orientation, an AraC-type transcription regulator (pegR). The peg operon was flanked by two different sets of transposases. These three strains contained large plasmids and the operon was located in one of the large plasmids in S. terrae. The peg genes could be detected in other PEG-degrading sphingomonads. These results suggest that the peg genes have evolved in a plasmid-mediated manner. An insertion of a transposon gene (pegF) between pegD and pegA in strain 203 was found, which caused the constitutive expression of pegA in this strain.

The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole

We determined the complete 254,797-bp nucleotide sequence of the plasmid pCAR3, a carbazole-degradative plasmid from Sphingomonas sp. strain KA1. A region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pNL1 isolated from the aromatic-degrading Novosphingobium aromaticivorans strain F199. The presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. Although pCAR3 is thought to carry clustered genes for conjugative transfer, a filter-mating assay between KA1 and a pCAR3-cured strain (KA1W) was unsuccessful, indicating that pCAR3 might be deficient in conjugative transfer. Several degradative genes were found on pCAR3, including two kinds of carbazole-degradative gene clusters (car-I and car-II), and genes for electron transfer components of initial oxygenase for carbazole (fdxI, fdrI, and fdrII). Putative genes were identified for the degradation of anthranilate (and), catechol (cat), 2-hydroxypenta-2,4-dienoate (carDFE), dibenzofuran/fluorene (dbf/fln), protocatechuate (lig), and phthalate (oph). It appears that pCAR3 may carry clustered genes (car-I, car-II, fdxI, fdrI, fdrII, and, and cat) for the degradation of carbazole into tricarboxylic acid cycle intermediates; KA1W completely lost the ability to grow on carbazole, and the carbazole-degradative genes listed above were all expressed when KA1 was grown on carbazole. Reverse transcription-PCR analysis also revealed that the transcription of car-I, car-II, and cat genes was induced by carbazole or its metabolic intermediate. Southern hybridization analyses with probes prepared from car-I, car-II, repA, parA, traI, and traD genes indicated that several Sphingomonas carbazole degraders have DNA regions similar to parts of pCAR3.

Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6

Sphingomonas xenophaga BN6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. A gene cluster was identified on the plasmid pBN6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. A DNA fragment of 16 915 bp was sequenced which contained 17 ORFs. The genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 2'-hydroxybenzalpyruvate aldolase of the naphthalenesulfonate pathway were identified on the DNA fragment and the encoded proteins heterologously expressed in Escherichia coli. Also, the genes encoding the ferredoxin and ferredoxin reductase of a multi-component, ring-hydroxylating naphthalenesulfonate dioxygenase were identified by insertional inactivation. The identified genes generally demonstrated the highest degree of homology to enzymes encoded by the phenanthrene-degrading organism Sphingomonas sp. P2, or the megaplasmid pNL1 of the naphthalene- and biphenyl-degrading strain Sphingomonas aromaticivorans F199. The genes of S. xenophaga BN6 participating in the degradation of naphthalenesulfonates also shared the same organization in three different transcriptional units as the genes involved in the degradation of naphthalene, biphenyl, and phenanthrene previously found in Sphingomonas sp. P2 and S. aromaticivorans F199. The genes were flanked in S. xenophaga BN6 by ORFs which specify proteins that show the highest homologies to proteins of mobile genetic elements.