Horizontal gene transfer of atrazine-degrading genes (atz) from Agrobacterium tumefaciens St96-4 pADP1::Tn5 to bacteria of maize-cultivated soil

Tracking atrazine degradation in soil combining 14C-mineralisation assays and compound-specific isotope analysis

The quantification of pesticide dissipation in agricultural soil is challenging. In this study, we investigated atrazine biodegradation in both liquid and soil experiments bioaugmented with distinct atrazine-degrading bacterial isolates. This was achieved by combining 14C-mineralisation assays and compound-specific isotope analysis of atrazine. In liquid experiments, the three bacterial isolates mineralised over 40% of atrazine, demonstrating their potential for extensive degradation. However, the kinetics of mineralisation and degradation varied among the isolates. Carbon stable isotope fractionation was similar for Pseudomonas isolates ADPT34 and ADP2T0, but slightly higher for Chelatobacter SR27. In soil experiments, atrazine primarily degraded into atrazine-desethyl, while atrazine-hydroxy was mainly observed in experiments with SR27. Atrazine mineralisation in soil by ADPT34 and SR27 exceeded 40%, whereas ADP2T0 exhibited a mineralisation rate of 10%. In experiments with ADPT34 and SR27, atrazine 14C-residues were predominantly found in the non-extractable fraction, whereas they accumulated in the extractable fraction in the experiment with ADP2T0. Compound-specific isotope analysis (CSIA) relies on changes of stable isotope ratios and holds potential to evaluate herbicide transformation in soil. CSIA of atrazine indicated atrazine biodegradation in water and solvent extractable soil fractions and varied between 29% and 52%, depending on the bacterial isolate. Despite atrazine degradation in both soil fractions, a significant portion of atrazine residues persisted, depending on the bacterial degrader, initial cell concentration, and mineralisation and degradation rates. Overall, our approach can aid in quantifying atrazine persistence and degradation in soil, and in optimizing bioaugmentation strategies for remediating soils contaminated with persistent herbicides.

Evaluating phytochemical and microbial contributions to atrazine degradation

The inclusion of warm-season grasses, such as switchgrass (Panicum virgatum) and eastern gamagrass (EG) (Tripsacum dactyloides), in vegetated buffer strips has been shown to mitigate herbicide contamination in runoff and increase herbicide degradation in soil. The mode of action by which buffer strip rhizospheres enhance herbicide degradation remains unclear, but microorganisms and phytochemicals are believed to facilitate degradation processes. The objectives of this study were to: 1) screen root extracts from seven switchgrass cultivars for the ability to degrade the herbicide atrazine (ATZ) in solution; 2) determine sorption coefficients (K_d) of the ATZ-degrading phytochemical 2-β-D-glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one (DBG) to soil and Ca-montmorillonite, and investigate if DBG or ATZ sorption alters degradation processes; and 3) quantify ATZ degradation rates and soil microbial response to ATZ application in mesocosms containing soil and select warm-season grasses. Phytochemicals extracted from the roots of switchgrass cultivars degraded 44-85% of ATZ in 16-h laboratory assays, demonstrating that some switchgrass cultivars could rapidly degrade ATZ under laboratory conditions. However, attempts to isolate ATZ-degrading phytochemicals from plant roots were unsuccessful. Sorption studies revealed that DBG was strongly sorbed to soil (K_d = 87.2 L kg^-1) and Ca-montmorillonite (K_d = 31.7 L kg^-1), and DBG driven hydrolysis of ATZ was entirely inhibited when either ATZ or DBG were sorbed to Ca-montmorillonite. Atrazine degradation rates in mesocosm soils were rapid (t_0.5 = 8.2-11.2 d), but not significantly different between soils collected from the two switchgrass cultivar mesocosms, the eastern gamagrass cultivar mesocosm, and the unvegetated mesocosm (control). Significant changes in three phospholipid fatty acid biomarkers were observed among the treatments. These changes indicated that different ATZ-degrading microbial consortia resulted in equivalent ATZ degradation rates between treatments. Results demonstrated that soil microbial response was the dominant mechanism controlling ATZ degradation in the soil studied, rather than root phytochemicals.

Labour sharing promotes coexistence in atrazine degrading bacterial communities

Microbial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

Background

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.

Methods

Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA.

Results

A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins.

Conclusions

Direct plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0868-3) contains supplementary material, which is available to authorized users.

Establishment of multiple pesticide biodegradation capacities from pesticide-primed materials in on-farm biopurification system microcosms treating complex pesticide-contaminated wastewater

BACKGROUND

On-farm biopurification systems (BPSs) treat pesticide-containing wastewater at farms by biodegradation and sorption processes. The inclusion of pesticide-primed material carrying a pesticide-degrading microbial community is beneficial for improving biodegradation, but no data exist for treating wastewater containing multiple pesticides, as often occurs on farms. In a microcosm set-up, an examination was carried out to determine whether multiple pesticide degradation activities could be simultaneously established in the matrix of a BPS by the simultaneous inclusion of different, appropriate pesticide-primed materials. The microcosms were fed with a mixture of pesticides including the fungicide metalaxyl and the herbicides bentazon, isoproturon, linuron and metamitron, and pesticide-degrading activities were monitored over time.

RESULTS

The strategy immediately provided the microcosms with a multiple pesticide degradation/mineralisation capacity, which improved during feeding of the pesticide mixture. Not only did the degradation of the parent compound improve but also that of the produced metabolites and compound mineralisation. The time to achieve maximum degradation/mineralisation capacity depended on the pesticide degradation capacity of the pesticide-primed materials.

CONCLUSIONS

The data obtained show that the addition of pesticide-primed materials into the matrix of a BPS as an approach to improve biodegradation can be extended to the treatment of pesticide mixtures.

Study of phenanthrene utilizing bacterial consortia associated with cowpea (Vigna unguiculata) root nodules

Many legumes have been selected as model plants to degrade organic contaminants with their special associated rhizosphere microbes in soil. However, the function of root nodules during microbe-assisted phytoremediation is not clear. A pot study was conducted to examine phenanthrene (PHE) utilizing bacteria associated with root nodules and the effects of cowpea root nodules on phytoremediation in two different types of soils (freshly contaminated soil and aged contaminated soil). Cowpea nodules in freshly-contaminated soil showed less damage in comparison to the aged-contaminated soil, both morphologically and ultra-structurally by scanning electron microscopy. The study of polycyclic aromatic hydrocarbon (PAH) attenuation conducted by high performance liquid chromatography revealed that more PAH was eliminated from liquid culture around nodulated roots than nodule-free roots. PAH sublimation and denaturation gradient gel electrophoresis were applied to analyze the capability and diversity of PAH degrading bacteria from the following four parts of rhizo-microzone: bulk soil, root surface, nodule surface and nodule inside. The results indicated that the surface and inside of cowpea root nodules were colonized with bacterial consortia that utilized PHE. Our results demonstrated that root nodules not only fixed nitrogen, but also enriched PAH-utilizing microorganisms both inside and outside of the nodules. Legume nodules may have biotechnological values for PAH degradation.

Evidence for cooperative mineralization of diuron by Arthrobacter sp. BS2 and Achromobacter sp. SP1 isolated from a mixed culture enriched from diuron exposed environments

Diuron was found to be mineralized in buffer strip soil (BS) and in the sediments (SED) of the Morcille river in the Beaujolais vineyard repeatedly treated with this herbicide. Enrichment cultures from BS and SED samples led to the isolation of three bacterial strains transforming diuron to 3,4-dichloroaniline (3,4-DCA) its aniline derivative. 16S rRNA sequencing revealed that they belonged to the genus Arthrobacter (99% of similarity to Arthrobacter globiformis strain K01-01) and were designated as Arthrobacter sp. BS1, BS2 and SED1. Diuron-degrading potential characterized by sequencing of the puhA gene, characterizing the diuron-degradaing potential, revealed 99% similarity to A. globiformis strain D47 puhA gene isolated a decade ago in the UK. These isolates were also able to use chlorotoluron for their growth. Although able to degrade linuron and monolinuron to related aniline derivatives they were not growing on them. Enrichment cultures led to the isolation of a strain from the sediments entirely degrading 3,4-DCA. 16S rRNA sequence analysis showed that it was affiliated to the genus Achromobacter (99% of similarity to Achromobacter sp. CH1) and was designated as Achromobacter sp. SP1. The dcaQ gene encoding enzyme responsible for the transformation of 3,4-DCA to chlorocatechol was found in SP1 with 99% similarity to that of Comamonas testosteroni WDL7. This isolate also used for its growth a range of anilines (3-chloro-4-methyl-aniline, 4-isopropylaniline, 4-chloroaniline, 3-chloroaniline, 4-bromoaniline). The mixed culture composed of BS2 and SP1 strains entirely mineralizes (14)C-diuron to (14)CO2. Diuron-mineralization observed in the enrichment culture could result from the metabolic cooperation between these two populations.

Microorganisms and Biotic Interactions

Most ecosystems are populated by a large number of diversified microorganisms, which interact with one another and form complex interaction networks. In addition, some of these microorganisms may colonize the surface or internal parts of plants and animals, thereby providing an additional level of interaction complexity. These microbial relations range from intraspecific to interspecific interactions, and from simple short-term interactions to intricate long-term ones. They have played a key role in the formation of plant and animal kingdoms, often resulting in coevolution; they control the size, activity level, and diversity patterns of microbial communities. Therefore, they modulate trophic networks and biogeochemical cycles, regulate ecosystem productivity, and determine the ecology and health of plant and animal partners. A better understanding of these interactions is needed to develop microbe-based ecological engineering strategies for environmental sustainability and conservation, to improve environment-friendly approaches for feed and food production, and to address health challenges posed by infectious diseases. The main types of biotic interactions are presented: interactions between microorganisms, interactions between microorganisms and plants, and interactions between microorganisms and animals.

Plant growth responses to inorganic environmental contaminants are density-dependent: experiments with copper sulfate, barley and lettuce

The density-dependence of terrestrial plant-plant interactions in the presence of toxins has previously been explored using biodegradable compounds. We exposed barley and lettuce to four copper concentrations at four stand densities. We hypothesized that toxin effects would decrease and Cu uptake would increase at increasing plant densities. We analyzed toxin effects by (a) comparing plant biomasses and (b) using a recent regression model that has a separate parameter for the interaction of resource competition and toxin interference. Plant response to Cu was density-dependent in both experiments. Total Cu uptake by barley increased and the dose per plant decreased as plant density increased. This study is the first to demonstrate that plant density mediates plant response to metals in soil in a predictable way. This highlights the need to explore the mechanisms for and consequences of these effects, and to integrate the use of several plant densities into standard ecotoxicological testing.

Cloning of a novel 6-chloronicotinic acid chlorohydrolase from the newly isolated 6-chloronicotinic acid mineralizing Bradyrhizobiaceae strain SG-6C

A 6-chloronicotinic acid mineralizing bacterium was isolated from enrichment cultures originating from imidacloprid-contaminated soil samples. This Bradyrhizobiaceae, designated strain SG-6C, hydrolytically dechlorinated 6-chloronicotinic acid to 6-hydroxynicotinic acid, which was then further metabolised via the nicotinic acid pathway. This metabolic pathway was confirmed by growth and resting cell assays using HPLC and LC-MS studies. A candidate for the gene encoding the initial dechlorination step, named cch2 (for 6-chloronicotinic acid chlorohydrolase), was identified using genome sequencing and its function was confirmed using resting cell assays on E. coli heterologously expressing this gene. The 464 amino acid enzyme was found to be a member of the metal dependent hydrolase superfamily with similarities to the TRZ/ATZ family of chlorohydrolases. We also provide evidence that cch2 was mobilized into this bacterium by an Integrative and Conjugative Element (ICE) that feeds 6-hydroxynicotinic acid into the existing nicotinic acid mineralization pathway.

Isolation and characterisation of a bacterial strain degrading the herbicide sulcotrione from an agricultural soil

BACKGROUND

The dissipation kinetics of the herbicide sulcotrione sprayed 4 times on a French soil was studied using a laboratory microcosm approach. An advanced cultivation-based method was then used to isolate the bacteria responsible for biotransformation of sulcotrione. Chromatographic methods were employed as complementary tools to define its metabolic pathway.

RESULTS

Soil microflora was able quickly to biotransform the herbicide (DT(50) ≈ 8 days). 2-Chloro-4-mesylbenzoic acid, one of its main metabolites, was clearly detected. However, no accelerated biodegradation process was observed. Eight pure sulcotrione-resistant strains were isolated, but only one (1OP) was capable of degrading this herbicide with a relatively high efficiency and to use it as a sole source of carbon and energy. In parallel, another sulcotrione-resistant strain (1TRANS) was shown to be incapable of degrading the herbicide. Amplified ribosomal restriction analysis (ARDRA) and repetitive extragenic palendromic PCR genomic (REP-PCR) fingerprinting of strains 1OP and 1TRANS gave indistinguishable profiles.

CONCLUSION

Sequencing and aligning analysis of 16S rDNA genes of each pure strain revealed identical sequences and a close phylogenetic relationship (99% sequence identity) to Pseudomonas putida. Such physiological and genetic properties of 1OP to metabolise sulcotrione were probably governed by mobile genetic elements in the genome of the bacteria.

In vitro evolution of an atrazine-degrading population under cyanuric acid selection pressure: evidence for the selective loss of a 47 kb region on the plasmid ADP1 containing the atzA, B and C genes

The adaptation of microorganisms to pesticide biodegradation relies on the recruitment of catabolic genes by horizontal gene transfer and homologous recombination mediated by insertion sequences (IS). This environment-friendly function is maintained in the degrading population but it has a cost which could diminish its fitness. The loss of genes in the course of evolution being a major mechanism of ecological specialization, we mimicked evolution in vitro by sub-culturing the atrazine-degrading Pseudomonas sp. ADP in a liquid medium containing cyanuric acid as the sole source of nitrogen. After 120 generations, a new population evolved, which replaced the original one. This new population grew faster on cyanuric acid but showed a similar cyanuric acid degrading ability. Plasmid profiles and Southern blot analyses revealed the deletion of a 47 kb region from pADP1 containing the atzABC genes coding for the enzymes that turn atrazine into cyanuric acid. Long PCR and sequencing analyses revealed that this deletion resulted from a homologous recombination between two direct repeats of a 110-bp, identical to ISPps1 of Pseudomonas huttiensis, flanking the deleted 47 kb region. The loss of a region containing three functional genes constitutively expressed thereby constituting a genetic burden under cyanuric acid selection pressure was responsible for the gain in fitness of the new population. It highlights the IS-mediated plasticity of the pesticide-degrading potential and shows that IS not only favours the expansion of the degrading genetic potential thanks to dispersion and duplication events but also contribute to its reduction thanks to deletion events.

Spatial distribution of enhanced atrazine degradation across northeastern Colorado cropping systems

Reports of enhanced atrazine degradation and reduced residual weed control have increased in recent years, sparking interest in identifying factors contributing to enhanced atrazine degradation. The objectives of this study were to (i) assess the spatial distribution of enhanced atrazine degradation in 45 commercial farm fields in northeastern Colorado (Kit Carson, Larimer, Logan, Morgan, Phillips, and Yuma counties) where selected cultural management practices and soil bio-chemo-physical properties were quantified; (ii) utilize Classification and Regression Tree (CART) Analysis to identify cultural management practices and (or) soil bio-chemophysical attributes that are associated with enhanced atrazine degradation; and (iii) translate our CART Analysis into a model that predicts relative atrazine degradation rate (rapid, moderate, or slow) as a function of known management practices and (or) soil properties. Enhanced atrazine degradation was widespread within a 300-km radius across northeastern Colorado, with approximately 44% of the fields demonstrating rapid atrazine degradation activity (laboratory-based dissipation time halflife [DT50] < 3 d). The most rapid degradation rates occurred in fields that received the most frequent atrazine applications. Classification and Regression Tree Analysis resulted in a prediction model that correctly classified soils with rapid atrazine DT50 80% of the time and soils with slow degradation (DT50 > 8 d) 62.5% of the time. Significant factors were recent atrazine use history, soil pH, and organic matter content. The presence/absence of atzC polymerase chain reaction (PCR) product was not a significant predictor variable for atrazine DT50. In conclusion, enhanced atrazine degradation is widespread in northeastern Colorado. If producers know their atrazine use history, soil pH, and OM content, they should be able to identify fields exhibiting enhanced atrazine degradation using our CART Model.

Agronomic and environmental implications of enhanced s-triazine degradation

Novel catabolic pathways enabling rapid detoxification of s-triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s-triazine mineralization, i.e. atzABCDEF and trzNDF, occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s-triazine herbicides for weed control, and, with the exception of acidic soil conditions and s-triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s-triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s-triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s-triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted.

Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil

AIMS

To characterize atrazine-degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes.

METHODS AND RESULTS

The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65-80% of (14) C ring-labelled atrazine. The presence of trzN-atzBC-trzD, trzN-atzABC-trzD and trzN-atzABCDEF-trzD gene combinations was determined by PCR. In all enriched communities, trzN-atzBC genes were located on a 165-kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α-, β- and γ-subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine-degrading community members previously isolated from the same contaminated site.

CONCLUSIONS

The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine-catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long-term contamination by s-triazine compounds.

Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent

AIMS

To characterize an atrazine-degrading bacterial community enriched from the wastewater of a herbicide factory.

METHODS AND RESULTS

The community mineralized 81.4 +/- 1.9% of [(14)C-ring]atrazine and 31.0 +/- 1.8% of [(14)C-ethyl]atrazine within 6 days of batch cultivation in mineral salts medium containing atrazine as the sole nitrogen source. Degradation activity of the community towards different chloro- and methylthio-substituted s-triazine compounds was also demonstrated. Restriction analysis of amplified 16S rDNA revealed high diversity of bacterial populations forming the community, with Pseudomonas species dominating in the clone library. Atrazine-degrading genetic potential of the community determined by PCR revealed the presence of trzN, atzB, atzC and trzD genes. The trzN, atzB and atzC genes were shown to be located on a plasmid of 322 kb. Quantitative PCR showed that relative abundances of atzB, atzC and trzD genes were approx. 100-fold lower than 16S rDNA.

CONCLUSIONS

The enriched community represents a complex bacterial association expressing substantial atrazine-mineralizing activity and a broad specificity towards a range of s-triazine compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study is beginning to yield insights into the richness, genetic potential and density of functional atrazine-mineralizing community that could be a potential bioaugmentation agent for improving biotransformation processes in wastewaters bearing different s-triazine compounds.

Bacteria associated with oak and ash on a TCE-contaminated site: characterization of isolates with potential to avoid evapotranspiration of TCE

BACKGROUND, AIM, AND SCOPE

Along transects under a mixed woodland of English Oak (Quercus robur) and Common Ash (Fraxinus excelsior) growing on a trichloroethylene (TCE)-contaminated groundwater plume, sharp decreases in TCE concentrations were observed, while transects outside the planted area did not show this remarkable decrease. This suggested a possibly active role of the trees and their associated bacteria in the remediation process. Therefore, the cultivable bacterial communities associated with both tree species growing on this TCE-contaminated groundwater plume were investigated in order to assess the possibilities and practical aspects of using these common native tree species and their associated bacteria for phytoremediation. In this study, only the cultivable bacteria were characterized because the final aim was to isolate TCE-degrading, heavy metal resistant bacteria that might be used as traceable inocula to enhance bioremediation.

MATERIALS AND METHODS

Cultivable bacteria isolated from bulk soil, rhizosphere, root, stem, and leaf were genotypically characterized by amplified rDNA restriction analysis (ARDRA) of their 16S rRNA gene and identified by 16S rRNA gene sequencing. Bacteria that displayed distinct ARDRA patterns were screened for heavy metal resistance, as well as TCE tolerance and degradation, as preparation for possible future in situ inoculation experiments. Furthermore, in situ evapotranspiration measurements were performed to investigate if the degradation capacity of the associated bacteria is enough to prevent TCE evapotranspiration to the air.

RESULTS AND DISCUSSION

Between both tree species, the associated populations of cultivable bacteria clearly differed in composition. In English Oak, more species-specific, most likely obligate endophytes were found. The majority of the isolated bacteria showed increased tolerance to TCE, and TCE degradation capacity was observed in some of the strains. However, in situ evapotranspiration measurements revealed that a significant amount of TCE and its metabolites was evaporating through the leaves to the atmosphere.

CONCLUSIONS AND PERSPECTIVES

The characterization of the isolates obtained in this study shows that the bacterial community associated with Oak and Ash on a TCE-contaminated site, was strongly enriched with TCE-tolerant strains. However, this was not sufficient to degrade all TCE before it reaches the leaves. A possible strategy to overcome this evapotranspiration to the atmosphere is to enrich the plant-associated TCE-degrading bacteria by in situ inoculation with endophytic strains capable of degrading TCE.

Laboratory degradation studies of 14C-atrazine and -isoproturon in soil from sugarcane cultivated fields under Kenyan tropical conditions

A study to compare the degradation rates of atrazine (6-chloro-N(2)-ethyl-N(4)-isopropyl-1,3,5-triazine-2,4-diammine) and isoproturon [3-(4-isopropylphenyl)-1,1-dimethylurea] in soils from sugarcane fields with different practices of herbicides application was carried out. (14)C-atrazine was poorly mineralized to (14)CO(2) (1.10% +/- 0.22%) after 139 days of incubation in soil without previous exposure to atrazine. In the same soil also with no previous isoproturon exposure isoproturon was mineralized to (14)CO(2) by 7.70% +/- 0.94%. Atrazine mineralization after 98 days was 13.4% +/- 0.30% in soil which discontinued the use of atrazine in 1997 while it was 89.9% +/- 1.23% in soil in which atrazine is currently being used. The isoproturon mineralization values were 7.24% +/- 0.85% and 22.97% +/- 0.96% in soil which discontinued atrazine and soil currently using atrazine, respectively.

Diversity of 'benzenetriol dioxygenase' involved in p-nitrophenol degradation in soil bacteria

Ring hydroxylating dioxygenases (RHDOs) are one of the most important classes of enzymes featuring in the microbial metabolism of several xenobiotic aromatic compounds. One such RHDO is benzenetriol dioxygenase (BtD) which constitutes the metabolic machinery of microbial degradation of several mono- phenolic and biphenolic compounds including nitrophenols. Assessment of the natural diversity of benzenetriol dioxygenase (btd) gene sequence is of great significance from basic as well as applied study point of view. In the present study we have evaluated the gene sequence variations amongst the partial btd genes that were retrieved from microorganisms enriched for PNP degradation from pesticide contaminated agriculture soils. The gene sequence analysis was also supplemented with an in silico restriction digestion analysis. Furthermore, a phylogenetic analysis based on the deduced amino acid sequence(s) was performed wherein the evolutionary relatedness of BtD enzyme with similar aromatic dioxygenases was determined. The results obtained in this study indicated that this enzyme has probably undergone evolutionary divergence which largely corroborated with the taxonomic ranks of the host microorganisms.

Application of fluorescence in situ hybridization technique to detect simazine-degrading bacteria in soil samples

We propose a new approach to evaluate the natural attenuation capacity of soil by using fluorescence in situ hybridization (FISH). A specific oligonucleotide probe AtzB1 was designed based on the sequence data of the atzB gene involved in the hydrolytic deamination of s-triazines; this gene, located in a multiple copy plasmid was detected by the optimized FISH protocol. Two agricultural soils (Lodi and Henares) with a history of simazine treatments, and two natural soils (Soto and Monza), without previous exposure to simazine, were studied. AtzB1 probe-target cells were found only in the agricultural soils and, in a greater percentage, in the Lodi soil, compared to the Henares one. Moreover, the greatest percentage of AtzB1 probe-target cells in Lodi was accompanied by a greater mineralization rate, compared to the Henares soil. The FISH method used in this study was suitable for the detection of simazine-degrading bacteria and could be a useful indicator of the potential of soil bioremediation.

Rapid mineralization of the phenylurea herbicide diuron by Variovorax sp. strain SRS16 in pure culture and within a two-member consortium

The phenylurea herbicide diuron [N-(3,4-dichlorophenyl)-N,N-dimethylurea] is widely used in a broad range of herbicide formulations, and consequently, it is frequently detected as a major water contaminant in areas where there is extensive use. We constructed a linuron [N-(3,4-dichlorophenyl)-N-methoxy-N-methylurea]- and diuron-mineralizing two-member consortium by combining the cooperative degradation capacities of the diuron-degrading organism Arthrobacter globiformis strain D47 and the linuron-mineralizing organism Variovorax sp. strain SRS16. Neither of the strains mineralized diuron alone in a mineral medium, but combined, the two strains mineralized 31 to 62% of the added [ring-U-(14)C]diuron to (14)CO(2), depending on the initial diuron concentration and the cultivation conditions. The constructed consortium was used to initiate the degradation and mineralization of diuron in soil without natural attenuation potential. This approach led to the unexpected finding that Variovorax sp. strain SRS16 was able to mineralize diuron in a pure culture when it was supplemented with appropriate growth substrates, making this strain the first known bacterium capable of mineralizing diuron and representatives of both the N,N-dimethyl- and N-methoxy-N-methyl-substituted phenylurea herbicides. The ability of the coculture to mineralize microgram-per-liter levels of diuron was compared to the ability of strain SRS16 alone, which revealed the greater extent of mineralization by the two-member consortium (31 to 33% of the added [ring-U-(14)C]diuron was mineralized to (14)CO(2) when 15.5 to 38.9 mug liter(-1) diuron was used). These results suggest that the consortium consisting of strains SRS16 and D47 could be a promising candidate for remediation of soil and water contaminated with diuron and linuron and their shared metabolite 3,4-dichloroaniline.

pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the beta-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices.

Isolation and characterization of novel atrazine-degrading microorganisms from an agricultural soil

Six previously undescribed microorganisms capable of atrazine degradation were isolated from an agricultural soil that received repeated exposures of the commonly used herbicides atrazine and acetochlor. These isolates are all Gram-positive and group with microorganisms in the genera Nocardioides and Arthrobacter, both of which contain previously described atrazine degraders. All six isolates were capable of utilizing atrazine as a sole nitrogen source when provided with glucose as a separate carbon source. Under the culture conditions used, none of the isolates could utilize atrazine as the sole carbon and nitrogen source. We used several polymerase-chain-reaction-based assays to screen for the presence of a number of atrazine-degrading genes and verified their identity through sequencing. All six isolates contain trzN and atzC, two well-characterized genes involved in the conversion of atrazine to cyanuric acid. An additional atrazine-degrading gene, atzB, was detected in one of the isolates as well, yet none appeared to contain atzA, a commonly encountered gene in atrazine impacted soils and atrazine-degrading isolates. Interestingly, the deoxyribonucleic acid sequences of trzN and atzC were all identical, implying that their presence may be the result of horizontal gene transfer among these isolates.

Molecular and population analyses of a recombination event in the catabolic plasmid pJP4

Cupriavidus necator JMP134(pJP4) harbors a catabolic plasmid, pJP4, which confers the ability to grow on chloroaromatic compounds. Repeated growth on 3-chlorobenzoate (3-CB) results in selection of a recombinant strain, which degrades 3-CB better but no longer grows on 2,4-dichlorophenoxyacetate (2,4-D). We have previously proposed that this phenotype is due to a double homologous recombination event between inverted repeats of the multicopies of this plasmid within the cell. One recombinant form of this plasmid (pJP4-F3) explains this phenotype, since it harbors two copies of the chlorocatechol degradation tfd gene clusters, which are essential to grow on 3-CB, but has lost the tfdA gene, encoding the first step in degradation of 2,4-D. The other recombinant plasmid (pJP4-FM) should harbor two copies of the tfdA gene but no copies of the tfd gene clusters. A molecular analysis using a multiplex PCR approach to distinguish the wild-type plasmid pJP4 from its two recombinant forms, was carried out. Expected PCR products confirming this recombination model were found and sequenced. Few recombinant plasmid forms in cultures grown in several carbon sources were detected. Kinetic studies indicated that cells containing the recombinant plasmid pJP4-FM were not selectable by sole carbon source growth pressure, whereas those cells harboring recombinant plasmid pJP4-F3 were selected upon growth on 3-CB. After 12 days of repeated growth on 3-CB, the complete plasmid population in C. necator JMP134 apparently corresponds to this form. However, wild-type plasmid forms could be recovered after growing this culture on 2,4-D, indicating that different plasmid forms can be found in C. necator JMP134 at the population level.

Genetic rearrangement of the atzAB atrazine-degrading gene cassette from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2

We report the characterization of the rearrangement phenomena responsible for the movement of the atrazine-degrading atzA and B genes from pADP1::Tn5 to the chromosome of Variovorax sp. MD1 and MD2. Long PCRs and Southern blot analyses revealed that the two genes forming a gene cassette moved in a unique rearrangement event. It also revealed that the boundaries of the plasmid sequence inserted in the chromosome correspond to IS1071or to sequences close to IS1071. It suggests that this genetic rearrangement could result from the transposition of the composite transposon delimited by IS1071 insertion sequences and containing atzA and atzB genes. In addition, for MD1 and MD2 strains the sequencing of the remaining sequence on pADP1::Tn5 indicated that the deletion of the atzA and B genes from the plasmid might be the result of a recombination event that occurred between the IS1071 insertion sequences surrounding the atzAB gene cassette.