Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

Fitness-Conditional Genes for Soil Adaptation in the Bioaugmentation Agent Pseudomonas veronii 1YdBTEX2

Strain inoculation (bioaugmentation) is a potentially useful technology to provide microbiomes with new functionalities. However, there is limited understanding of the genetic factors contributing to successful establishment of inoculants. This work aimed to characterize the genes implicated in proliferation of the monoaromatic compound-degrading Pseudomonas veronii 1YdBTEX2 in nonsterile polluted soils. We generated two independent mutant libraries by random minitransposon-delivered marker insertion followed by deep sequencing (Tn-seq) with a total of 5.0 × 10⁵ unique insertions. Libraries were grown in multiple successive cycles for up to 50 generations either in batch liquid medium or in two types of soil microcosms with different resident microbial content (sand or silt) in the presence of toluene. Analysis of gene insertion abundances at different time points (passed generations of metapopulation growth), in comparison to proportions at start and to in silico generated randomized insertion distributions, allowed to define ~800 essential genes common to both libraries and ~2,700 genes with conditional fitness effects in either liquid or soil (195 of which resulted in fitness gain). Conditional fitness genes largely overlapped among all growth conditions but affected approximately twice as many functions in liquid than in soil. This indicates soil to be a more promiscuous environment for mutant growth, probably because of additional nutrient availability. Commonly depleted genes covered a wide range of biological functions and metabolic pathways, such as inorganic ion transport, fatty acid metabolism, amino acid biosynthesis, or nucleotide and cofactor metabolism. Only sparse gene sets were uncovered whose insertion caused fitness decrease exclusive for soils, which were different between silt and sand. Despite detectable higher resident bacteria and potential protist predatory counts in silt, we were, therefore, unable to detect any immediately obvious candidate genes affecting P. veronii biological competitiveness. In contrast to liquid growth conditions, mutants inactivating flagella biosynthesis and motility consistently gained strong fitness advantage in soils and displayed higher growth rates than wild type. In conclusion, although many gene functions were found to be important for growth in soils, most of these are not specific as they affect growth in liquid minimal medium more in general. This indicates that P. veronii does not need major metabolic reprogramming for proliferation in soil with accessible carbon and generally favorable growth conditions. IMPORTANCE Restoring damaged microbiomes is still a formidable challenge. Classical widely adopted approaches consist of augmenting communities with pure or mixed cultures in the hope that these display their intended selected properties under in situ conditions. Ecological theory, however, dictates that introduction of a nonresident microbe is unlikely to lead to its successful proliferation in a foreign system such as a soil microbiome. In an effort to study this systematically, we used random transposon insertion scanning to identify genes and possibly, metabolic subsystems, that are crucial for growth and survival of a bacterial inoculant (Pseudomonas veronii) for targeted degradation of monoaromatic compounds in contaminated nonsterile soils. Our results indicate that although many gene functions are important for proliferation in soil, they are general factors for growth and not exclusive for soil. In other words, P. veronii is a generalist that is not a priori hindered by the soil for its proliferation and would make a good bioaugmentation candidate.

Responses of Bacterial Taxonomical Diversity Indicators to Pollutant Loadings in Experimental Wetland Microcosms

Urbanization results in higher stormwater loadings of pollutants such as metals and nutrients into surface waters. This directly impacts organisms in aquatic ecosystems, including microbes. Sediment microbes are known for pollution reduction in the face of contamination, making bacterial communities an important area for bioindicator research. This study explores the pattern of bacterial responses to metal and nutrient pollution loading and seeks to evaluate whether bacterial indicators can be effective as a biomonitoring risk assessment tool for wetland ecosystems. Microcosms were built containing sediments collected from wetlands in the urbanizing Pike River watershed in southeastern Wisconsin, USA, with metals and nutrients added at 7 day intervals. Bacterial DNA was extracted from the microcosm sediments, and taxonomical profiles of bacterial communities were identified up to the genera level by sequencing 16S bacterial rRNA gene (V3–V4 region). Reduction of metals (example: 90% for Pb) and nutrients (example: 98% for NO3−) added in water were observed. The study found correlations between diversity indices of genera with metal and nutrient pollution as well as identified specific genera (including Fusibacter, Aeromonas, Arthrobacter, Bacillus, Bdellovibrio, and Chlorobium) as predictive bioindicators for ecological risk assessment for metal pollution.

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils

BACKGROUND

Bioaugmentation aims to use the capacities of specific bacterial strains inoculated into sites to enhance pollutant biodegradation. Bioaugmentation results have been mixed, which has been attributed to poor inoculant growth and survival in the field, and, consequently, moderate catalytic performance. However, our understanding of biodegradation activity mostly comes from experiments conducted under laboratory conditions, and the processes occurring during adaptation and invasion of inoculants into complex environmental microbiomes remain poorly known. The main aim of this work was thus to study the specific and different cellular reactions of an inoculant for bioaugmentation during adaptation, growth and survival in natural clean and contaminated non-sterile soils, in order to better understand factors limiting bioaugmentation.

RESULTS

As inoculant we focused on the monoaromatic compound-degrading bacterium Pseudomonas veronii 1YdBTEX2. The strain proliferated in all but one soil types in presence and in absence of exogenously added toluene. RNAseq and differential genome-wide gene expression analysis illustrated both a range of common soil responses such as increased nutrient scavenging and recycling, expression of defense mechanisms, as well as environment-specific reactions, notably osmoprotection and metal homeostasis. The core metabolism of P. veronii remained remarkably constant during exponential growth irrespective of the environment, with slight changes in cofactor regeneration pathways, possibly needed for balancing defense reactions.

CONCLUSIONS

P. veronii displayed a versatile global program, enabling it to adapt to a variety of soil environments in the presence and even in absence of its target pollutant toluene. Our results thus challenge the widely perceived dogma of poor survival and growth of exogenous inoculants in complex microbial ecosystems such as soil and provide a further basis to developing successful bioaugmentation strategies.

Environmental connectivity controls diversity in soil microbial communities

Interspecific interactions are thought to govern the stability and functioning of microbial communities, but the influence of the spatial environment and its structural connectivity on the potential of such interactions to unfold remain largely unknown. Here we studied the effects on community growth and microbial diversity as a function of environmental connectivity, where we define environmental connectivity as the degree of habitat fragmentation preventing microbial cells from living together. We quantitatively compared growth of a naturally-derived high microbial diversity community from soil in a completely mixed liquid suspension (high connectivity) to growth in a massively fragmented and poorly connected environment (low connectivity). The low connectivity environment consisted of homogenously-sized miniature agarose beads containing random single or paired founder cells. We found that overall community growth was the same in both environments, but the low connectivity environment dramatically reduced global community-level diversity compared to the high connectivity environment. Experimental observations were supported by community growth modeling. The model predicts a loss of diversity in the low connectivity environment as a result of negative interspecific interactions becoming more dominant at small founder species numbers. Counterintuitively for the low connectivity environment, growth of isolated single genotypes was less productive than that of random founder genotype cell pairs, suggesting that the community as a whole profited from emerging positive interspecific interactions. Our work demonstrates the importance of environmental connectivity for growth of natural soil microbial communities, which aids future efforts to intervene in or restore community composition to achieve engineering and biotechnological objectives.

Manupriyam Dubey et al. use experimental systems with naturally derived soil microbiomes in liquid suspensions and encapsulated beads to compare community dynamics in well-connected and poorly connected environments. While their results show that microbial growth does not vary between conditions, they report that low connectivity led to reduced microbial diversity and suggest that these reductions in microbial diversity may be due to increased negative interspecific interactions.

Uncovering Competitive and Restorative Effects of Macro- and Micronutrients on Sodium Benzoate Biodegradation

A model aromatic compound, sodium benzoate, is generally used for simulating aromatic pollutants present in textile effluents. Bioremediation of sodium benzoate was studied using the most abundant bacteria, Pseudomonas citronellolis, isolated from the effluent treatment plants of South Gujarat, India. Multiple nutrients constituting the effluent in actual conditions are proposed to have interactive effects on biodegradation which needs to be analyzed strategically for successful field application of developed bioremediation process. Two explicitly different sets of fractional factorial designs were used to investigate the interactive influence of alternative carbon, nitrogen sources, and inorganic micronutrients on sodium benzoate degradation. The process was negatively influenced by the co-existence of other carbon sources and higher concentration of KH₂PO₄ whereas NH₄Cl and MgSO₄ exhibited positive effects. Optimized concentrations of NH₄Cl, MgSO₄, and KH₂PO₄ were found to be 0.35, 1.056, and 0.3 mg L^–1 respectively by central composite designing. The negative effect of high amount of KH₂PO₄ could be ameliorated by increasing the amount of NH₄Cl in the biodegradation milieu indicating the possibility of restoration of the degradation capability for sodium benzoate degradation in the presence of higher phosphate concentration.

Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation

We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, organisms related to Azoarcus spp. were identified as key players in the degradation of toluene and ethylbenzene. An organism highly related to Georgfuchsia toluolica G5G6 was enriched with p-xylene, a particularly recalcitrant compound. The anaerobic degradation of p-xylene requires a metabolic trait that was not described for members of the genus Georgfuchsia before. In line with this, we were able to identify a putative 4-methylbenzoyl-CoA reductase gene cluster in the respective enrichment culture, which is possibly involved in the anaerobic degradation of p-xylene.

Aislamiento e identificación de levaduras degradadoras de hidrocarburos aromáticos, presentes en tanques de gasolina de vehículos urbanos

Se obtuvieron aislamientos de levaduras a partir de muestreos en tanques de combustible de vehículos urbanos, con el objeto de evaluar su potencial actividad de degradación de hidrocarburos aromáticos derivados del petróleo. Se realizaron ensayos de crecimiento en medio mínimo mineral sólido utilizando distintos hidrocarburos (benceno, tolueno, naftaleno, fenantreno, y pireno). Los aislamientos que presentaron crecimiento notorio en alguno de los hidrocarburos aromáticos policíclicos fueron identificados mediante secuenciación Sanger de los marcadores moleculares ITS1 e ITS2 del ARNr. Se obtuvieron 16 aislados de levaduras, de las cuales tres presentaron crecimiento conspicuo con hidrocarburos aromáticos como única fuente de carbono. Las cepas identificadas pertenecen al género Rhodotorula y corresponden a las especies Rhodotorula calyptogenae (99,8% de identidad) y Rhodotorula dairenensis (99,8% de identidad). Dichas cepas presentaron crecimiento en benceno, tolueno, naftaleno, fenantreno.  En este estudio se reporta por primera vez la presencia de levaduras del género Rhodotorula que habitan los ductos y tanques de gasolina de vehículos urbanos, así como su capacidad para utilizar distintos hidrocarburos aromáticos que son contaminantes para el medio ambiente. Estos resultados sugieren que dichas levaduras constituyen potenciales candidatos para la degradación de éstos compuestos, como parte de estrategias de biorremediación.

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors

Bacteria are often found tolerating polluted environments. Such bacteria may be exploited to bioremediate contaminants in controlled ex situ reactor systems. One potential strategic goal of such systems is to harness microbes directly from the environment such that they exhibit the capacity to markedly degrade organic pollutants of interest. Here, the use of biofilm cultivation techniques to inoculate and activate moving bed biofilm reactor (MBBR) systems for the degradation of polycyclic aromatic hydrocarbons (PAHs) was explored. Biofilms were cultivated from 4 different hydrocarbon contaminated sites using a minimal medium spiked with the 16 EPA identified PAHs. Overall, all 4 inoculant sources resulted in biofilm communities capable of tolerating the presence of PAHs, but only 2 of these exhibited enhanced PAH catabolic gene prevalence coupled with significant degradation of select PAH compounds. Comparisons between inoculant sources highlighted the dependence of this method on appropriate inoculant screening and biostimulation efforts.

Candidate nematicidal proteins in a new Pseudomonas veronii isolate identified by its antagonistic properties against Xiphinema index

The nematode Xiphinema index affects grape vines and transmits important viruses associated with fanleaf degeneration. Pseudomonas spp. are an extensive bacterial group in which important biodegradation and/or biocontrol properties can occur for several strains in the group. The aim of this study was to identify new Pseudomonas isolates with antagonist activity against X. index. Forty bacterial isolates were obtained from soil and root samples from Chilean vineyards. Thirteen new fluorescent pseudomonads were found and assessed for their antagonistic capability. The nematicide Pseudomonas protegens CHA0 was used as a control. Challenges of nematode individuals in King's B semi-solid agar Petri dishes facilitated the identification of the Pseudomonas veronii isolate R4, as determined by a 16S rRNA sequence comparison. This isolate was as effective as CHA0 as an antagonist of X. index, although it had a different lethality kinetic. Milk-induced R4 cultures exhibited protease and lipase activities in cell supernatants using both gelatin/tributyrin Petri dish assays and zymograms. Three proteins with these activities were isolated and subjected to mass spectrometry. Amino acid partial sequences enabled the identification of a 49-kDa protease similar to metalloprotease AprA and two lipases of 50 kDa and 69 kDa similar to LipA and ExoU, respectively. Electron microscopy analyses of challenged nematodes revealed degraded cuticle after R4 supernatant treatment. These results represent a new and unexplored property in this species associated with the presence of secretable lipases and protease, similar to characterized enzymes present in biocontrol pseudomonads.

The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand

The natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (BTEX) may be accelerated by inoculation of specific biodegraders (bioaugmentation). Bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. In order to better understand the adaptive response of cells during a transition to contaminated material, we analyzed here the genome and short-term (1 h) changes in genome-wide gene expression of the BTEX-degrading bacterium Pseudomonas veronii 1YdBTEX2 in non-sterile soil and liquid medium, both in presence or absence of toluene. We obtained a gapless genome sequence of P. veronii 1YdBTEX2 covering three individual replicons with a total size of 8 Mb, two of which are largely unrelated to current known bacterial replicons. One-hour exposure to toluene, both in soil and liquid, triggered massive transcription (up to 208-fold induction) of multiple gene clusters, such as toluene degradation pathway(s), chemotaxis and toluene efflux pumps. This clearly underlines their key role in the adaptive response to toluene. In comparison to liquid medium, cells in soil drastically changed expression of genes involved in membrane functioning (e.g., lipid composition, lipid metabolism, cell fatty acid synthesis), osmotic stress response (e.g., polyamine or trehalose synthesis, uptake of potassium) and putrescine metabolism, highlighting the immediate response mechanisms of P. veronii 1YdBTEX2 for successful establishment in polluted soil.

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR.

Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station

Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes were related to (i) nidA3 of Mycobacterium sp. py146, (ii) pdoA of Terrabacter sp. HH4, (iii) nidA of Diaphorobacter sp. KOTLB, and (iv) pdoA2 of Mycobacterium sp. CH-2, with 95-99% similarity. Clone libraries of Gram-negative RHD genes were related to the following: (i) naphthalene dioxygenase of Burkholderia glathei, (ii) phnAc of Burkholderia sartisoli, and (iii) RHD alpha subunit of uncultured bacterium, with 41-46% similarity. Interestingly, the diversity of the Gram-positive RHD genes found around this area was higher than those of the Gram-negative RHD genes. Real-time PCR showed different abundance of dioxygenase genes between locations. Moreover, the PCR-denaturing gradient gel electrophoresis (DGGE) profile demonstrated diverse bacterial populations, according to their location. Forty dominant fragments in the DGGE profiles were excised and sequenced. All of the sequences belonged to ten bacterial phyla: Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Cyanobacteria, Chlorobium, and Acidobacteria. In addition, the bacterial genus Sphingomonas, which has been suggested to be one of the major PAH degraders in the environment, was observed in some locations. The results demonstrated that indigenous bacteria have the potential ability to degrade PAHs and provided information to support the conclusion that bioremediation processes can occur in the Antarctic soils and sediments studied here.

AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics

Understanding prokaryotic transformation of recalcitrant pollutants and the in-situ metabolic nets require the integration of massive amounts of biological data. Decades of biochemical studies together with novel next-generation sequencing data have exponentially increased information on aerobic aromatic degradation pathways. However, the majority of protein sequences in public databases have not been experimentally characterized and homology-based methods are still the most routinely used approach to assign protein function, allowing the propagation of misannotations. AromaDeg is a web-based resource targeting aerobic degradation of aromatics that comprises recently updated (September 2013) and manually curated databases constructed based on a phylogenomic approach. Grounded in phylogenetic analyses of protein sequences of key catabolic protein families and of proteins of documented function, AromaDeg allows query and data mining of novel genomic, metagenomic or metatranscriptomic data sets. Essentially, each query sequence that match a given protein family of AromaDeg is associated to a specific cluster of a given phylogenetic tree and further function annotation and/or substrate specificity may be inferred from the neighboring cluster members with experimentally validated function. This allows a detailed characterization of individual protein superfamilies as well as high-throughput functional classifications. Thus, AromaDeg addresses the deficiencies of homology-based protein function prediction, combining phylogenetic tree construction and integration of experimental data to obtain more accurate annotations of new biological data related to aerobic aromatic biodegradation pathways. We pursue in future the expansion of AromaDeg to other enzyme families involved in aromatic degradation and its regular update.

Database URL:http://aromadeg.siona.helmholtz-hzi.de

Support vector regression model of wastewater bioreactor performance using microbial community diversity indices: effect of stress and bioaugmentation

The relationship between microbial community structure and function has been examined in detail in natural and engineered environments, but little work has been done on using microbial community information to predict function. We processed microbial community and operational data from controlled experiments with bench-scale bioreactor systems to predict reactor process performance. Four membrane-operated sequencing batch reactors treating synthetic wastewater were operated in two experiments to test the effects of (i) the toxic compound 3-chloroaniline (3-CA) and (ii) bioaugmentation targeting 3-CA degradation, on the sludge microbial community in the reactors. In the first experiment, two reactors were treated with 3-CA and two reactors were operated as controls without 3-CA input. In the second experiment, all four reactors were additionally bioaugmented with a Pseudomonas putida strain carrying a plasmid with a portion of the pathway for 3-CA degradation. Molecular data were generated from terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S rRNA and amoA genes from the sludge community. The electropherograms resulting from these T-RFs were used to calculate diversity indices - community richness, dynamics and evenness - for the domain Bacteria as well as for ammonia-oxidizing bacteria in each reactor over time. These diversity indices were then used to train and test a support vector regression (SVR) model to predict reactor performance based on input microbial community indices and operational data. Considering the diversity indices over time and across replicate reactors as discrete values, it was found that, although bioaugmentation with a bacterial strain harboring a subset of genes involved in the degradation of 3-CA did not bring about 3-CA degradation, it significantly affected the community as measured through all three diversity indices in both the general bacterial community and the ammonia-oxidizer community (α = 0.5). The impact of bioaugmentation was also seen qualitatively in the variation of community richness and evenness over time in each reactor, with overall community richness falling in the case of bioaugmented reactors subjected to 3-CA and community evenness remaining lower and more stable in the bioaugmented reactors as opposed to the unbioaugmented reactors. Using diversity indices, 3-CA input, bioaugmentation and time as input variables, the SVR model successfully predicted reactor performance in terms of the removal of broad-range contaminants like COD, ammonia and nitrate as well as specific contaminants like 3-CA. This work was the first to demonstrate that (i) bioaugmentation, even when unsuccessful, can produce a change in community structure and (ii) microbial community information can be used to reliably predict process performance. However, T-RFLP may not result in the most accurate representation of the microbial community itself, and a much more powerful prediction tool can potentially be developed using more sophisticated molecular methods.

Cloning and mutagenesis of catechol 2,3-dioxygenase gene from the gram-positive Planococcus sp. strain S5

In this study, the catechol 2,3-dioxygenase gene that encodes a 307- amino-acid protein was cloned from Planococcus sp. S5. The protein was identified to be a member of the superfamily I, subfamily 2A of extradiol dioxygenases. In order to study residues and regions affecting the enzyme's catalytic parameters, the c23o gene was randomly mutated by error-prone PCR. The wild-type enzyme and mutants containing substitutions within either the C-terminal or both domains were functionally produced in Escherichia coli and their activity towards catechol was characterized. The C23OB65 mutant with R296Q substitution showed significant tolerance to acidic pH with an optimum at pH 5.0. In addition, it showed activity more than 1.5 as high as that of the wild type enzyme and its Km was 2.5 times lower. It also showed altered sensitivity to substrate inhibition. The results indicate that residue at position 296 plays a role in determining pH dependence of the enzyme and its activity. Lower activity toward catechol was shown for mutants C23OB58 and C23OB81. Despite lower activity, these mutants showed higher affinity to catechol and were more sensitive to substrate concentration than nonmutated enzyme.

Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2

Pseudomonas veronii strain 1YdBTEX2 was isolated from a benzene-contaminated site. Here we report the draft genome sequence of 1YdBTEX2 and its genes associated with aromatic metabolism. The broad catabolic potential of this strain is consistent with the environment from which it was isolated.

De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes

Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.

Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system

Despite various efforts to develop tools to detect and compare the catabolic potential and activity for pollutant degradation in environmental samples, there is still a need for an open-source, curated and reliable array method. We developed a custom array system including a novel normalization strategy that can be applied to any microarray design, allowing the calculation of the reliability of signals and make cross-experimental comparisons. Array probes, which are fully available to the scientific community, were designed from knowledge-based curated databases for key aromatic catabolic gene families and key alkane degradation genes. This design assigns signals to the respective protein subfamilies, thus directly inferring function and substrate specificity. Experimental procedures were optimized using DNA of four genome sequenced biodegradation strains and reliability of signals assessed through a novel normalization procedure, where a plasmid containing four artificial targets in increased copy numbers and co-amplified with the environmental DNA served as an internal calibration curve. The array system was applied to assess the catabolic gene landscape and transcriptome of aromatic contaminated environmental samples, confirming the abundance of catabolic gene subfamilies previously detected by functional metagenomics but also revealing the presence of previously undetected catabolic groups and specifically their expression under pollutant stress.

In vitro degradation of fluoranthene by bacteria isolated from petroleum sludge

An investigation was carried out for in vitro degradation of fluoranthene by four bacterial strains (PSM6, PSM7, PSM10 and PSM11) isolated from the petroleum sludge. Although all the strains registered their growth in MSM with 100 ppm fluoranthene, PSM11 growth was better than other strains. Growth of bacterial strains invariably corresponded to their degradation potential of fluoranthene. After 168 h of incubation, 61% fluoranthene was degraded by PSM11, followed by PSM10 (48%) and PSM6 (42%) and the least was recorded in PSM7 (41%). Besides, 11% loss in fluoranthene was attributed to abiotic factors. Thirty-eight times more activity of catechol 2,3-dioxygenase than catechol 1,2-dioxygenase showed that it played a significant role in fluoranthene degradation. Molecular weight of catechol 2,3-dioxygenase isolated from PSM11 was determined as ∼ 136 kDa by size exclusion chromatography and 34 kDa on denaturing SDS-PAGE, indicating tetrameric nature of the enzyme.

Bacterial diversity dynamics in a long-term petroleum-contaminated soil

Bacterial diversity dynamics were investigated in the soil samples in different distances and depths from/at a long-term petroleum-contaminated site. Microbial activity in the soil samples showed ATP values closely correlated with organic matter content (OC) and total petroleum hydrocarbon (TPH). Bacterial community diversity (H) and evenness (J) using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and PCR-T-RFLP (terminal restriction fragment length polymorphism) results showed positive correlation with concentration of TPH or OC, but tmoA (toluene monooxygenase gene)-based bacterial H and J using a PCR-T-RFLP result did not. No significant difference of H and J values in the bacterial and the tmoA communities was observed. The bacterial community structure characterized by PCR-DGGE and PCR-T-RFLP techniques showed similarity according to soil sampling distance rather than soil sampling depth. Canonical correspondence analysis demonstrated that OC including TPH had the most significant effect on the bacterial community diversity at the long-term petroleum-contaminated site.

Microbial communities to mitigate contamination of PAHs in soil--possibilities and challenges: a review

BACKGROUND, AIM, AND SCOPE

Although highly diverse and specialized prokaryotic and eukaryotic microbial communities in soil degrade polycyclic aromatic hydrocarbons (PAHs), most of these are removed slowly. This review will discuss the biotechnological possibilities to increase the microbial dissipation of PAHs from soil as well as the main biological and biotechnological challenges.

DISCUSSION AND CONCLUSIONS

Microorganism provides effective and economically feasible solutions for soil cleanup and restoration. However, when the PAHs contamination is greater than the microbial ability to dissipate them, then applying genetically modified microorganisms might help to remove the contaminant. Nevertheless, it is necessary to have a more holistic review of the different individual reactions that are simultaneously taking place in a microbial cell and of the interactions microorganism-microorganism, microorganism-plant, microorganism-soil, and microorganisms-PAHs.

PERSPECTIVES

Elucidating the function of genes from the PAHs-polluted soil and the study in pure cultures of isolated PAHs-degrading organisms as well as the generation of microorganisms in the laboratory that will accelerate the dissipation of PAHs and their safe application in situ have not been studied extensively. There is a latent environmental risk when genetically engineered microorganisms are used to remedy PAHs-contaminated soil.

A permeable reactive barrier for the bioremediation of BTEX-contaminated groundwater: Microbial community distribution and removal efficiencies

This study was conducted with column experiments, batch experiments, and bench-scale permeable reactive barrier (PRB) for monitoring the PRB in the relation between BTEX (benzene, toluene, ethylbenzene, and p-xylene) decomposition efficiency and the distribution of a microbial community. To obtain the greatest amount of dissolved oxygen from oxygen-releasing compounds (ORCs), 20-d column tests were conducted, the results of which showed that the highest average amount of dissolved oxygen (DO) of 5.08 mg l(-1) (0.25 mg-O(2)d(-1)g(-1)-ORC) was achieved at a 40% level of CaO(2). In the batch experiments, the highest concentrations of benzene and toluene in which these compounds could be completely degraded were assumed to be 80 mg l(-1). Long-term monitoring for a PRB indicated that ORCs made with the oxygen-releasing rate of 0.25 mg-O(2)d(-1)g(-1)-ORC were applicable for use in the PRB because these ORCs have a long-term effect and adequately meet the oxygen demand of bacteria. The results from the DGGE of 16S rDNAs and real-time PCR of catechol 2,3-dioxygenase gene revealed the harmful effects of shock-loading on the microbial community and reduction in the removal efficiencies of BTEX. However, the efficiencies in the BTEX decomposition were improved and the microbial activities could be recovered thereafter as evidenced by the DGGE results.

Modified 3-oxoadipate pathway for the biodegradation of methylaromatics in Pseudomonas reinekei MT1

Catechols are central intermediates in the metabolism of aromatic compounds. Degradation of 4-methylcatechol via intradiol cleavage usually leads to the formation of 4-methylmuconolactone (4-ML) as a dead-end metabolite. Only a few microorganisms are known to mineralize 4-ML. The mml gene cluster of Pseudomonas reinekei MT1, which encodes enzymes involved in the metabolism of 4-ML, is shown here to encode 10 genes found in a 9.4-kb chromosomal region. Reverse transcription assays revealed that these genes form a single operon, where their expression is controlled by two promoters. Promoter fusion assays identified 4-methyl-3-oxoadipate as an inducer. Mineralization of 4-ML is initiated by the 4-methylmuconolactone methylisomerase encoded by mmlI. This reaction produces 3-ML and is followed by a rearrangement of the double bond catalyzed by the methylmuconolactone isomerase encoded by mmlJ. Deletion of mmlL, encoding a protein of the metallo-beta-lactamase superfamily, resulted in a loss of the capability of the strain MT1 to open the lactone ring, suggesting its function as a 4-methyl-3-oxoadipate enol-lactone hydrolase. Further metabolism can be assumed to occur by analogy with reactions known from the 3-oxoadipate pathway. mmlF and mmlG probably encode a 4-methyl-3-oxoadipyl-coenzyme A (CoA) transferase, and the mmlC gene product functions as a thiolase, transforming 4-methyl-3-oxoadipyl-CoA into methylsuccinyl-CoA and acetyl-CoA, as indicated by the accumulation of 4-methyl-3-oxoadipate in the respective deletion mutant. Accumulation of methylsuccinate by an mmlK deletion mutant indicates that the encoded acetyl-CoA hydrolase/transferase is crucial for channeling methylsuccinate into the central metabolism.

Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome

Pseudomonas putida GJ31 has been reported to grow on chlorobenzene using a meta-cleavage pathway with chlorocatechol 2,3-dioxygenase (CbzE) as a key enzyme. The CbzE-encoding gene was found to be localized on the 180 kb plasmid pKW1 in a cbzTEXGS cluster, which is flanked by transposases and encodes only a partial (chloro)catechol meta-cleavage pathway comprising ferredoxin reductase, chlorocatechol 2,3-dioxygenase, an unknown protein, 2-hydroxymuconic semialdehyde dehydrogenase and glutathione S-transferase. Downstream of cbzTEXGS are located cbzJ, encoding a novel type of 2-hydroxypent-2,4-dienoate hydratase, and a transposon region highly similar to Tn5501. Upstream of cbzTEXGS, traNEOFG transfer genes were found. The search for gene clusters possibly completing the (chloro)catechol metabolic pathway of GJ31 revealed the presence of two additional catabolic gene clusters on pKW1. The mhpRBCDFETP cluster encodes enzymes for the dissimilation of 2,3-dihydroxyphenylpropionate in a novel arrangement characterized by the absence of a gene encoding 3-(3-hydroxyphenyl)propionate monooxygenase and the presence of a GntR-type regulator, whereas the nahINLOMKJ cluster encodes part of the naphthalene metabolic pathway. Transcription studies supported their possible involvement in chlorobenzene degradation. The upper pathway cluster, comprising genes encoding a chlorobenzene dioxygenase and a chlorobenzene dihydrodiol dehydrogenase, was localized on the chromosome. A high level of transcription in response to chlorobenzene revealed it to be crucial for chlorobenzene degradation. The chlorobenzene degradation pathway in strain GJ31 is thus a mosaic encoded by four gene clusters.

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.

Characterization of a gene cluster involved in 4-chlorocatechol degradation by Pseudomonas reinekei MT1

Pseudomonas reinekei MT1 has previously been reported to degrade 4- and 5-chlorosalicylate by a pathway with 4-chlorocatechol, 3-chloromuconate, 4-chloromuconolactone, and maleylacetate as intermediates, and a gene cluster channeling various salicylates into an intradiol cleavage route has been reported. We now report that during growth on 5-chlorosalicylate, besides a novel (chloro)catechol 1,2-dioxygenase, C12O(ccaA), a novel (chloro)muconate cycloisomerase, MCI(ccaB), which showed features not yet reported, was induced. This cycloisomerase, which was practically inactive with muconate, evolved for the turnover of 3-substituted muconates and transforms 3-chloromuconate into equal amounts of cis-dienelactone and protoanemonin, suggesting that it is a functional intermediate between chloromuconate cycloisomerases and muconate cycloisomerases. The corresponding genes, ccaA (C12O(ccaA)) and ccaB (MCI(ccaB)), were located in a 5.1-kb genomic region clustered with genes encoding trans-dienelactone hydrolase (ccaC) and maleylacetate reductase (ccaD) and a putative regulatory gene, ccaR, homologous to regulators of the IclR-type family. Thus, this region includes genes sufficient to enable MT1 to transform 4-chlorocatechol to 3-oxoadipate. Phylogenetic analysis showed that C12O(ccaA) and MCI(ccaB) are only distantly related to previously described catechol 1,2-dioxygenases and muconate cycloisomerases. Kinetic analysis indicated that MCI(ccaB) and the previously identified C12O(salD), rather than C12O(ccaA), are crucial for 5-chlorosalicylate degradation. Thus, MT1 uses enzymes encoded by a completely novel gene cluster for degradation of chlorosalicylates, which, together with a gene cluster encoding enzymes for channeling salicylates into the ortho-cleavage pathway, form an effective pathway for 4- and 5-chlorosalicylate mineralization.

Separation of DNA by capillary electrophoresis

This chapter reports an overview of the analytical techniques used to perform genetic analysis of polymerase chain reaction products using capillary electrophoresis. Three separate but related techniques are described: the separation of native DNA with detection using fluorescent intercalating dyes, the separation of denatured DNA using fluorescently labeled primers, and the detection of single-strand conformation polymorphisms using denatured DNA separated under native conditions. The various techniques involve electrokinetic injection of the DNA onto a narrow band at the head of the column, sieving the DNA through various entangled polymer matrices, and detection via single or multichannel laser-induced fluorescence. Analytical protocols are provided, and a series of representative electropherograms are included.

Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment

A bacterial strain capable of degrading some monochlorinated dibenzofurans, designated RW16T, was isolated from aerobic River Elbe sediments. The strain was characterized based on 16S rRNA gene sequence analysis, DNA G+C content, physiological characteristics, polyamines, ubiquinone and polar lipid pattern and fatty acid composition. This analysis revealed that strain RW16T represents a novel species of the genus Sphingobium. The DNA G+C content of strain RW16T, 60.7 mol%, is the lowest yet reported for the genus. 16S rRNA gene sequence analysis placed strain RW16T as an outlier in the genus Sphingobium. The name Sphingobium aromaticiconvertens sp. nov. is proposed for this dibenzofuran-mineralizing organism, with type strain RW16T (=DSM 12677T=CIP 109198T).

Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas

Bacterial isolates obtained from polychlorophenol-contaminated sites in Finland (strain K101T) and from a Dutch drinking water well (strain A175T) were characterized taxonomically. 16S rRNA gene sequence analysis, determination of DNA G+C content, physiological characterization, estimation of the ubiquinone and polar lipid patterns and fatty acid content revealed that strains K101T and A175T were similar to Sphingomonas wittichii RW1T but also showed pronounced differences. The DNA G+C contents of the two novel strains were 63.6 and 66.1 mol%, respectively. On the basis of these results, two novel species of the genus Sphingomonas are described, for which the names Sphingomonas haloaromaticamans sp. nov. [type strain A175T (=DSM 13477T=CCUG 53463T)] and Sphingomonas fennica sp. nov. [type strain K101T (=DSM 13665T=CCUG 53462T)] are proposed.

Widespread capacity to metabolize polychlorinated biphenyls by diverse microbial communities in soils with no significant exposure to PCB contamination

The purpose of this work was to determine the extent of microbial metabolic potential for polychlorinated biphenyls (PCBs) in soils that have had no previous exposure to this class of xenobiotic pollutants. Soil and sediment samples of distinct characteristics from six sites in Germany were used to inoculate PCB oil (Aroclor 1242) microdroplets. All samples yielded multispecies biofilms, as revealed by single-strand conformation polymorphism (SSCP) analyses of polymerase chain reaction (PCR) analysis of 16S rRNA genes, and sequence analysis of the main amplicons. Microbes representing 20 different operational taxonomic units (OTUs) were identified in the biofilms, but only a few were common to all biofilms, namely those closely related to Aquabacterium sp., Caulobacter sp., Imtechium assamiensis, Nevskia ramosa, Parvibaculum lavamentivorans and Burkholderia sp. The PCB biofilm communities were always distinct from control biofilms developing from the same samples in the absence of PCB. All PCB droplet-grown biofilms degraded multiple PCB congeners but differed in the congener spectra they degraded. These findings reveal that microbial potential to degrade PCBs is widespread in soils that have not been subjected to PCB contamination, and that this potential is characteristic of consortia of very diverse phylogenetic composition.

Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples

Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic alpha-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.

Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker

Benzylsuccinate synthase (Bss) is the key enzyme of anaerobic toluene degradation and has been found in all anaerobic toluene degrading bacterial isolates tested. However, only a few pure cultures capable of anaerobic toluene oxidation are available to date, and it is important to understand the relevance of these model organisms for in situ bioremediation of hydrocarbon-contaminated aquifers. Due to their phylogenetic dispersal, it is not possible to specifically target anaerobic toluene degraders using marker rRNA genes. We therefore established an assay targeting a approximately 794 bp fragment within the Bss alpha-subunit (bssA) gene, which allows for the specific detection and affiliation of both known and unknown anaerobic degraders. Three distinct tar-oil-contaminated aquifer sites were screened for intrinsic bssA gene pools in order to identify and compare the diversity of hydrocarbon degraders present at these selected sites. We were able to show that local diversity patterns of degraders were entirely distinct, apparently highly specialized and well-adapted to local biogeochemical settings. Discovered at one of the sites were bssA genes closely related to that of Geobacter spp., which provides evidence for an importance of iron reduction for toluene degradation in these sediments. Retrieved from the other two sites, dominated by sulfate reduction, were previously unidentified bssA genes and also deeply branching putative bssA homologues. We provide evidence for a previously unrecognized diversity of anaerobic toluene degraders and also of other hydrocarbon degraders using fumarate-adding key reactions in contaminated aquifers. These findings enhance our current understanding of intrinsic hydrocarbon-degrading microbial communities in perturbed aquifers and may have potential for the future assessment and prediction of natural attenuation based on degradation genes.

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment

Molecular approaches aimed at detection of a broad-range of prokaryotes in the environment routinely rely on classifying heterogeneous 16S rRNA genes amplified by polymerase chain reaction (PCR) using primers with broad specificity. The general method of sampling and categorizing DNA has been to clone then sequence the PCR products. However, the number of clones required to adequately catalog the majority of taxa in a sample is unwieldy. Alternatively, hybridizing target sequences to a universal 16S rRNA gene microarray may provide a more rapid and comprehensive view of prokaryotic community composition. This study investigated the breadth and accuracy of a microarray in detecting diverse 16S rRNA gene sequence types compared to clone-and-sequencing using three environmental samples: urban aerosol, subsurface soil, and subsurface water. PCR products generated from universal 16S rRNA gene-targeted primers were classified by using either the clone-and-sequence method or by hybridization to a novel high-density microarray of 297,851 probes complementary to 842 prokaryotic subfamilies. The three clone libraries comprised 1391 high-quality sequences. Approximately 8% of the clones could not be placed into a known subfamily and were considered novel. The microarray results confirmed the majority of clone-detected subfamilies and additionally demonstrated greater amplicon diversity extending into phyla not observed by the cloning method. Sequences matching operational taxonomic units within the phyla Nitrospira, Planctomycetes, and TM7, which were uniquely detected by the array, were verified with specific primers and subsequent amplicon sequencing. Subfamily richness detected by the array corresponded well with nonparametric richness predictions extrapolated from clone libraries except in the water community where clone-based richness predictions were greatly exceeded. It was concluded that although the microarray is unreliable in identifying novel prokaryotic taxa, it reveals greater diversity in environmental samples than sequencing a typically sized clone library. Furthermore, the microarray allowed samples to be rapidly evaluated with replication, a significant advantage in studies of microbial ecology.

TOL plasmid transfer during bacterial conjugation in vitro and rhizoremediation of oil compounds in vivo

Molecular profiling methods for horizontal transfer of aromatics-degrading plasmids were developed and applied during rhizoremediation in vivo and conjugations in vitro. pWW0 was conjugated from Pseudomonas to Rhizobium. The xylE gene was detected both in Rhizobium galegae bv. officinalis and bv. orientalis, but it was neither stably maintained in orientalis nor functional in officinalis. TOL plasmids were a major group of catabolic plasmids among the bacterial strains isolated from the oil-contaminated rhizosphere of Galega orientalis. A new finding was that some Pseudomonas migulae and Pseudomonas oryzihabitans strains harbored a TOL plasmid with both pWW0- and pDK1-type xylE gene. P. oryzihabitans 29 had received the archetypal TOL plasmid pWW0 from Pseudomonas putida PaW85. As an application for environmental biotechnology, the biodegradation potential of oil-polluted soil and the success of bioremediation could be estimated by monitoring changes not only in the type and amount but also in transfer of degradation plasmids.

A gene cluster involved in degradation of substituted salicylates via ortho cleavage in Pseudomonas sp. strain MT1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate

Pseudomonas sp. strain MT1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. Genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. One of the gene clusters characterized (sal) showed a novel gene arrangement, with salA, encoding a salicylate 1-hydroxylase, being clustered with salCD genes, encoding muconate cycloisomerase and catechol 1,2-dioxygenase, respectively, and was expressed during growth on salicylate and chlorosalicylate. A second gene cluster (cat), exhibiting the typical catRBCA arrangement of genes of the catechol branch of the 3-oxoadipate pathway in Pseudomonas strains, was expressed during growth on salicylate. Despite their high sequence similarities with isoenzymes encoded by the cat gene cluster, the catechol 1,2-dioxygenase and muconate cycloisomerase encoded by the sal cluster showed unusual kinetic properties. Enzymes were adapted for turnover of 4-chlorocatechol and 3-chloromuconate; however, 4-methylcatechol and 3-methylmuconate were identified as the preferred substrates. Investigation of the substrate spectrum identified 4- and 5-methylsalicylate as growth substrates, which were effectively converted by enzymes of the sal cluster into 4-methylmuconolactone, followed by isomerization to 3-methylmuconolactone. The function of the sal gene cluster is therefore to channel both chlorosubstituted and methylsubstituted salicylates into a catechol ortho cleavage pathway, followed by dismantling of the formed substituted muconolactones through specific pathways.

Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments

Soluble di-iron monooxygenases (SDIMOs) are key enzymes in the bacterial oxidation of hydrocarbons, and have applications in environmental and industrial biotechnology. SDIMOs from pure cultures are unlikely to represent the total diversity of this enzyme family, so we used polymerase chain reaction to survey the diversity of SDIMO alpha subunit genes in environmental samples, ethene enrichments and ethene-degrading bacterial isolates. From 178 cloned amplicons, 98 restriction fragment length polymorphism types were seen, from which 75 representative SDIMO sequences were obtained; 45 from environmental samples, 25 from enrichments and seven from isolates. The sequences were diverse, including genes similar to ethene (etnC), propene (amoC, pmoC), propane (prmA) and butane (bmoX) monooxygenases, in addition to many novel sequences comprising a new SDIMO group (group 6). Environmental samples showed the highest diversity, with strong representation of group 6 SDIMOs and prmA-like genes. Ethene stimulation of samples resulted in increased frequencies of group 4 SDIMOs (etnC-like). Four ethene-utilizing Mycobacterium isolates (NBB1-NBB4) from enrichments all contained etnC; one isolate (NBB4) also contained three additional SDIMO genes (bmoX-like, amoC-like and group 6). The primers, database, clone libraries and strains reported here provide a resource for future bioremediation and biocatalysis studies, with particular relevance for chlorinated alkene and alkane compounds.

Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases

The PCR-single-strand conformation polymorphism (SSCP) technique was used to assess the diversity and distribution of Rieske nonheme iron oxygenases of the toluene/biphenyl subfamily in soil DNA and bacterial isolates recovered from sites contaminated with benzene, toluene, ethylbenzene, and xylenes (BTEX). The central cores of genes encoding the catalytic alpha subunits were targeted, since they are responsible for the substrate specificities of these enzymes. SSCP functional genotype fingerprinting revealed a substantial diversity of oxygenase genes in three differently BTEX-contaminated soil samples, and sequence analysis indicated that in both the soil DNA and the bacterial isolates, genes for oxygenases related to the isopropylbenzene (cumene) dioxygenase branch of the toluene/biphenyl oxygenase subfamily were predominant among the detectable genotypes. The peptide sequences of the two most abundant alpha subunit sequence types differed by only five amino acids (residues 258, 286, 288, 289, and 321 according to numbering in cumene dioxygenase alpha subunit CumA1 of Pseudomonas fluorescens IP01). However, a strong correlation between sequence type and substrate utilization pattern was observed in isolates harboring these genes. Two of these residues were located at positions contributing, according to the resolved crystal structure of cumene dioxygenase from Pseudomonas fluorescens IP01, to the inner surface of the substrate-binding pocket. Isolates containing an alpha subunit with isoleucine and leucine at positions 288 and 321, respectively, were capable of degrading benzene and toluene, whereas isolates containing two methionine substitutions were found to be incapable of degrading toluene, indicating that the more bulky methionine residues significantly narrowed the available space within the substrate-binding pocket.