Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile.

This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (-3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of -6.3 to -8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment.IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions.

In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.

Subsurface nitrate reduction under wetlands takes place in narrow superficial zones.

This study aims to investigate the depth distribution of the Nitrate Reduction Potential (NRP) on a natural and a re-established wetland. The obtained NRP provides a valuable data of the driving factors affecting denitrification, the Dissimilatory Nitrate Reduction to Ammonium (DNRA) process and the performance of a re-established wetland. Intact soil cores were collected and divided in slices for the determination of Organic Matter (OM) through Loss of Ignition (LOI) as well as Dissolved Organic Carbon (DOC) and NRP spiking nitrate in batch tests. The Nitrate Reduction (NR) was fitted as a pseudo-first order rate constant (k) from where NRPs were obtained. NR took place in a narrow superficial zone showing a dropping natural logarithmic trend along depth. The main driving factor of denitrification, besides depth, was OM. Although, DOC and LOI could not express by themselves and absolute correlation with NRP, high amounts of DOC ensured enough quantity and quality of labile OM for NR. Besides, high concentration of LOI but a scarce abundance of DOC failed to drive NR. DNRA was only important in superficial samples with high contents of OM. Lastly, the high NRP of the re-established wetland confirms that wetlands can be restored satisfactorily.

Long-term dynamics of the atrazine mineralization potential in surface and subsurface soil in an agricultural field as a response to atrazine applications.

The dynamics of the atrazine mineralization potential in agricultural soil was studied in two soil layers (topsoil and at 35-45 cm depth) in a 3 years field trial to examine the long term response of atrazine mineralizing soil populations to atrazine application and intermittent periods without atrazine and the effect of manure treatment on those processes. In topsoil samples, (14)C-atrazine mineralization lag times decreased after atrazine application and increased with increasing time after atrazine application, suggesting that atrazine application resulted into the proliferation of atrazine mineralizing microbial populations which decayed when atrazine application stopped. Decay rates appeared however much slower than growth rates. Atrazine application also resulted into the increase of the atrazine mineralization potential in deeper layers which was explained by the growth on leached atrazine as measured in soil leachates recovered from that depth. However, no decay was observed during intermittent periods without atrazine application in the deeper soil layer. atzA and trzN gene quantification confirmed partly the growth and decay of the atrazine degrading populations in the soil and suggested that especially trzN bearing populations are the dominant atrazine degrading populations in both topsoil and deeper soil. Manure treatment only improved the atrazine mineralization rate in deeper soil layers. Our results point to the importance of the atrazine application history on a field and suggests that the long term survival of atrazine degrading populations after atrazine application enables them to rapidly proliferate once atrazine is again applied.

Genetic labelling and application of the isoproturon-mineralizing Sphingomonas sp. strain SRS2 in soil and rhizosphere.

AIMS: To construct a luxAB-labelled Sphingomonas sp. strain SRS2 maintaining the ability to mineralize the herbicide isoproturon and usable for monitoring the survival and distribution of strain SRS2 on plant roots in laboratory systems. METHODS AND RESULTS: We inserted the mini-Tn5-luxAB marker into strain SRS2 using conjugational mating. In the transconjugant mutants luciferase was produced in varying levels. The mutants showed significant differences in their ability to degrade isoproturon. One luxAB-labelled mutant maintained the ability to mineralize isoproturon and was therefore selected for monitoring colonization of barley roots. CONCLUSIONS: We successfully constructed a genetically labelled isoproturon-mineralizing-strain SRS2 and demonstrated its ability to survive in soil and its colonization of rhizosphere. SIGNIFICANCE AND IMPACT OF THE STUDY: The construction of a luxAB-labelled strain SRS2 maintaining the degradative ability, provides a powerful tool for ecological studies serving as the basis for evaluating SRS2 as a bioremediation agent.

Mineralization of aged atrazine and mecoprop in soil and aquifer chalk.

The effect of ageing on the bioavailability and sorption of the herbicides atrazine and mecoprop was studied in soil and aquifer chalk sampled at an agricultural field near Aalborg, Denmark. The herbicides were incubated in sterile soil or chalk up to 3 months prior to inoculation with 5 x 10(7) cells g(-1) (dry weight) of a mecoprop degrading highly enriched culture (PM) or 1 x 10(9) cells g(-1) (dry weight) of the atrazine degrading Pseudomonas sp. strain ADP. As a measure of the bioavailable residues accumulated 14CO2 was measured for 2 months. In both soil and chalk ageing limited the rate of atrazine mineralization, and in chalk the extent of mineralization was reduced as well. The fraction of sorbed atrazine in the soil ranged between 50% and 62%, whereas a maximum of 12% was sorbed in chalk. No impact on the mineralization of aged mecoprop was seen as no sorption of this herbicide on either soil or chalk was measured.

Biodegradation of the phenylurea herbicide isoproturon and its metabolites in agricultural soils.

Degradation of the phenylurea herbicide isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea) and several phenylurea and aniline metabolites was studied in agricultural soils previously exposed to isoproturon. The potential for degradation of the demethylated metabolite 3-(4-isopropylphenyl)-1-methylurea in the soils was much higher compared to isoproturon. In the most active soil only 6% of added 14C-labelled isoproturon was mineralised to 14CO2 within 20 days while in the same period 45% of added 14C-labelled 3-(4-isopropylphenyl)-1-methylurea was mineralized. This indicates that the initial N-demethylation may be a limiting step in the complete mineralization of isoproturon. Repeated addition of 3-(4-isopropylphenyl)-1-methylurea to the soil and further subculturing in mineral medium led to a highly enriched mixed bacterial culture with the ability to mineralize 3-(4-isopropylphenyl)-1-methylurea. The culture did not degrade either isoproturon or the didemethylated metabolite 3-(4-isopropylphenyl)-urea when provided as sole source of carbon and energy. The metabolite 4-isopropyl-aniline was also degraded and utilised for growth, thus indicating that 3-(4-isopropylphenyl)-1-methylurea is degraded by an initial cleavage of the methylurea-group followed by mineralization of the phenyl-moiety. Several attempts were made to isolate pure bacterial cultures degrading 3-(4-isopropylphenyl)-1-methylurea or 4-isopropyl-aniline, but they were not successful.

Isolation from agricultural soil and characterization of a Sphingomonas sp. able to mineralize the phenylurea herbicide isoproturon.

A soil bacterium (designated strain SRS2) able to metabolize the phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was isolated from a previously IPU-treated agricultural soil. Based on a partial analysis of the 16S rRNA gene and the cellular fatty acids, the strain was identified as a Sphingomonas sp. within the alpha-subdivision of the proteobacteria. Strain SRS2 was able to mineralize IPU when provided as a source of carbon, nitrogen, and energy. Supplementing the medium with a mixture of amino acids considerably enhanced IPU mineralization. Mineralization of IPU was accompanied by transient accumulation of the metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, and 4-isopropyl-aniline identified by high-performance liquid chromatography analysis, thus indicating a metabolic pathway initiated by two successive N-demethylations, followed by cleavage of the urea side chain and finally by mineralization of the phenyl structure. Strain SRS2 also transformed the dimethylurea-substituted herbicides diuron and chlorotoluron, giving rise to as-yet-unidentified products. In addition, no degradation of the methoxy-methylurea-substituted herbicide linuron was observed. This report is the first characterization of a pure bacterial culture able to mineralize IPU.

Mineralization and co-metabolic degradation of phenoxyalkanoic acid herbicides by a pure bacterial culture isolated from an aquifer.

A mecoprop [(+/-)-2-(4-chloro-2-methylphenoxy)propionic acid; MCPP]-degrading bacterium identified as Stenotrophomonas maltophilia PM was isolated from a Danish aquifer. Besides mecoprop, the bacterium was also able to degrade MCPA [(4-chloro-2-methylphenoxy)acetic acid)], MCPB [(4-chloro-2-methylphenoxy)butyric acid], 4-CPA [(4-chlorophenoxy)acetic acid], 2, 4-D [(2, 4-dichlorophenoxy)acetic acid], 2, 4-DP [(+/-)-2-(2, 4-dichlorophenoxy)propionic acid] and 2, 4-DB [(2, 4-dichlorophenoxy)butyric acid]. The bacterium was able to grow using these individual phenoxyalkanoic acids as the sole source of carbon and energy. In addition, it was able to co-metabolically degrade the phenoxyalkanoic acid 2, 4, 5-T [(2, 4, 5-trichlorophenoxy)acetic acid)] in the presence of mecoprop. At high 2, 4, 5-T concentrations (100 and 52 mg/l), however, only partial degradation of both mecoprop and 2, 4, 5-T was obtained, thus indicating the production of toxic metabolites. Bacterial yields were highest when grown on the monochlorinated phenoxyalkanoic acids as compared to the dichlorinated analogues, an exception being growth on 4CPA, which resulted in the lowest yield at all. Using [ring-U-14C]-labeled herbicides it was shown that the lower yield on 2, 4-D than on mecoprop was accompanied by greater CO2 generation, thus indicating that less energy is available from the complete oxidation of the dichlorinated phenoxyalkanoic acids than the monochlorinated analogues.

Degradation of herbicides in two sandy aquifers under different redox conditions.

We examined the potential for complete degradation (mineralisation) of the four [ring-U-14C]herbicides mecoprop, isoproturon, atrazine, and metsulphuron-methyl in two sandy aquifers representing aerobic, denitrifying, sulphate-reducing, and methanogenic conditions. Slurries with sediment and groundwater were set-up aerobically or anaerobically in the presence of the electron-acceptor prevailing at the sampling site, amended with 25 microg l(-1) herbicide, and incubated at 10 degrees C. Considerable mineralisation was only observed in sediment from the plough layer incubated aerobically. Here, 30% of 14C-mecoprop was recovered as 14CO2 after 15 days and 15% of isoproturon was recovered as 14CO2 after 267 days. Only 7% of mecoprop was recovered as 14CO2 after 313 days in sediment from the aquifer below sampled at 1.95-3.00 mbs (m below the surface). In denitrifying and methanogenic slurries, 3% of 14C added as mecoprop was recovered as 14CO2. Isoproturon was not mineralised except in the aerobic plough layer, and atrazine and metsulphuron-methyl were not mineralised under any of the conditions applied.

Degradation of herbicides in shallow Danish aquifers: an integrated laboratory and field study.

Degradation of pesticides in aquifers has been evaluated based on a number of co-ordinated field and laboratory studies carried out in Danish aquifers. These studies included investigations of vertical and horizontal variability in degradation rates from the vadose zone to an aquifer, the effects of aerobic versus anaerobic conditions, and the importance of concentration on degradation kinetics for a selected range of herbicides. The studies were based on different experimental approaches ranging from simple batch experiments to column studies to field injection experiments and, where appropriate, results were compared. Some herbicides were degraded under aerobic conditions (some phenoxy acids, DNOC and glyphosate) and others under aerobic conditions (other phenoxy acids, DNOC; there was some indication of atrazine transformation). Certain pesticides were not degraded in any investigations (dichlobenil, the dichlobenil metabolite 2,6-dichlorobenzamide (BAM), bentazone, isoproturon, metamitron and metsulfuron-methyl). The spatial variability was substantial, since hardly any of the investigated pesticides were degraded in all comparable samples. This means that it is very difficult to claim that a given pesticide is readily degradable in aquifers. However, the experimental approaches used (with incubations lasting more than a year) may not be sensitive enough to verify the low degradation rates that may be significant as a result of the long retention time of groundwaters.

Mineralization of 2,4-D, mecoprop, isoproturon and terbuthylazine in a chalk aquifer.

The potential to mineralize 2,4-dichlorophenoxyacetic acid (2,4-D), mecoprop, isoproturon and terbuthylazine was studied in soil and aquifer chalk sampled at an agricultural field near Aalborg, Denmark. Laboratory microcosms were incubated for 258 days under aerobic conditions at 10 degrees C with soil and chalk from 0.15-4.45 m below the surface. The [ring-U-14C]-labeled herbicides were added to obtain a concentration of 6 micrograms kg-1 and mineralization was measured as evolved [14C]carbon dioxide. The herbicides were readily mineralized in soil from the plough layer, except for terbuthylazine, which was mineralized only to a limited extent. In the chalk, lag periods of at least 40 days were observed, and a maximum of 51%, 33% and 6% of the added 2,4-D, mecoprop and isoproturon, respectively, were recovered as [14C]carbon dioxide. Large variations in both rate and extent of mineralization were observed within replicates in chalk. No mineralization of terbuthylazine in chalk was observed. As a measure of the general metabolic activity towards aromatic compounds, [ring-U-14C]-benzoic acid was included. It was readily mineralized at all depths.

Potential mineralization of four herbicides in a ground water--fed wetland area.

Herbicides may leach from agricultural fields into ground water feeding adjacent wetlands. However, only little is known of the fate of herbicides in wetland areas. The purpose of the study was to examine the potential of a riparian fen to mineralize herbides that could leach from an adjacent catchment area. Slurries were prepared from sediment and ground water collected from different parts of a wetland representing different redox conditions. The slurries were amended with O2, NO3-, SO4(2-), and CO2, or CO2 alone as electron acceptors to simulate the in situ conditions and their ability to mineralize the herbides mecoprop, metsulfuron-methyl, isoproturon and atrazine. In addition, the abundance of bacteria able to utilize O2, NO3-, SO4(2-) + CO2, and CO2 as electron acceptors was investigated along with the O2-reducing and methanogenic potential of the sediment. The recalcitrance to bacterial degradation depended on both the type of herbicide and the redox conditions pertaining. Mecoprop was the most readily degraded herbicide, with 36% of [ring-U-14C]mecoprop being mineralized to 14CO2 under aerobic conditions after 473 d. In comparison, approximately 29% of [phenyl-U-14C]metsulfuron-methyl and 16% of [ring-U-14C]isoproturon mineralized in aerobic slurries during the same period. Surprisingly, 8 to 13% of mecoprop also mineralized under anaerobic conditions. Neither metsulfuron-methyl nor isoproturon were mineralized under anaerobic conditions and atrazine was not mineralized under any of the redox conditions examined. The present study is the first to report mineralization of meco-prop in ground water in a wetland area, and the first to report mineralization of a phenoxyalcanoic acid herbicide under both aerobic and anaerobic conditions.

A quantitative enzyme-linked immunoassay for the detection of 2, 6-dichlorobenzamide (BAM), a degradation product of the herbicide dichlobenil.

2,6-Dichlorobenzamide (BAM) is the dominant degradation product in soil of the widely used herbicide dichlobenil. To detect BAM in water, a highly sensitive and specific enzyme-linked immunosorbent assay (ELISA) was developed. As an alternative to conventional coating of ELISA plates, the assay is based on direct covalent immobilisation. We achieved a surface which requires a short time for the immobilisation of ligand, is stable under dry storage, and which permits assays with a low CV. The performance of the assay was demonstrated by an inter-well CV that was generally less than 6%, a detection limit (DL(15)) of 0.02 microg/l and an IC(50) of 0.19 microg/l. Cross-reactivity was measured against nine analytes with structural homology to BAM. The highest degree of cross-reactivity (10.8%) was seen with 2,6-dichlorothiobenzamide (Chlorthiamid). Considering an EU-limit of 0.1 microg/l as the permissible maximum for the presence of pesticides in drinking water, this ELISA-procedure is suitable for large-scale screening of water samples suspected of being contaminated with BAM.

Isolation and immunocytochemical location of the nitrite-oxidizing system in nitrospira moscoviensis

A membrane-associated nitrite-oxidizing system of Nitrospira moscoviensis was isolated from heat-treated membranes. The four major proteins of the enzyme fraction had apparent molecular masses of 130, 62, 46, and 29 kDa, respectively. The nitrite-oxidizing activity was dependent on the presence of molybdenum. In contrast to the nitrite oxidoreductase of Nitrobacter hamburgensis X14, the activity of the nitrite-oxidizing system of Ns. moscoviensis increased when solubilized by heat treatment. Electron microscopy of the purified enzyme revealed uniform particles with a size of approximately 7 x 9 nm. SDS-immunoblotting analysis of crude extracts showed that the monoclonal antibodies Hyb 153-3, which recognize the beta-subunit of the nitrite oxidoreductase from Nitrobacter, reacted with a protein of 50 kDa in Ns. moscoviensis. This protein corresponded to the protein of 46 kDa of the purified enzyme and contained a b-type cytochrome. Using electron microscopic immunocytochemistry and the monoclonal antibodies Hyb 153-3, the nitrite-oxidizing system of Ns. moscoviensis was shown to be located in the periplasmic space. Here a periodic arrangement of membrane-associated particles was found on the outside of the cytoplasmic membrane in the form of a hexagonal pattern. It is supposed that these particles represent the nitrite-oxidizing system in Nitrospira.

Monoclonal antibodies recognizing nitrite oxidoreductase of Nitrobacter hamburgensis, N. winogradskyi, and N. vulgaris.

Three monoclonal antibodies (MAbs) against nitrite oxidoreductase (NOR) of Nitrobacter hamburgensis were produced. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting analysis of the purified enzyme showed that the MAbs named Hyb 153.1 and Hyb 153.3 both recognized a protein with a molecular mass of 64,000 Da, while Hyb 153.2 recognized a protein with a molecular mass of 115,000 Da. The molecular masses of these proteins are in the same range as those of the proteins of the alpha (115,000-Da) or beta (65,000-Da) subunit of the NOR. By using the antibodies, the amount of NOR was shown to be dependent on the growth conditions. The highest level of NOR was observed in N. hamburgensis when cells were growing mixotrophically. Analysis of whole-cell extracts of N. hamburgensis, N. winogradskyi, and N. vulgaris indicated serological homology of the NORs from these species of the genus Nitrobacter. The immunological analysis enables detection of the key enzyme of the genus Nitrobacter.

Chaperone-mediated activation in vivo of a Pseudomonas cepacia lipase.

An extracellular Pseudomonas cepacia lipase, LipA, is inactive when expressed in the absence of the product of the limA gene. Evidence has been presented that LimA is a molecular chaperone. The lipA and limA genes have been cloned in separate and independently inducible expression systems in Escherichia coli. These systems were used to test the molecular chaperone hypothesis by investigating whether LimA could activate presynthesized prelipase and whether presynthesized LimA could activate newly synthesized prelipase. The results show that LimA cannot activate presynthesized prelipase and that presynthesized LimA can activate only a limited number of de novo synthesized prelipase molecules. Co-immunoprecipitation of prelipase/lipase with LimA generated a 1:1 complex of prelipase/lipase and LimA. The results suggest that a 1:1 complex of LipA and LimA is required for prelipase processing and secretion of active lipase.

Activation of a bacterial lipase by its chaperone.

The gene lipA of Pseudomonas cepacia DSM 3959 encodes a prelipase from which a signal peptide is cleaved during secretion, producing a mature extracellular lipase. Expression of lipase in several heterologous hosts depends on the presence of another gene, limA, in cis or in trans. Lipase protein has been overproduced in Escherichia coli in the presence and absence of the lipase modulator gene limA. Therefore, limA is not required for the transcription of lipA or for the translation of the lipA mRNA. However, no lipase activity is observed in the absence of limA. limA has been overexpressed and encodes a 33-kDa protein, Lim. If lipase protein is denatured in 8 M urea and the urea is removed by dialysis, lipase activity is quantitatively recovered provided Lim protein is present during renaturation. Lip and Lim proteins form a complex precipitable either by an anti-lipase or anti-Lim antibody. The Lim protein has therefore the properties of a chaperone.

Effects of sulfuroxy anions on degradation of pentachlorophenol by a methanogenic enrichment culture.

We studied the degradation of pentachlorophenol (PCP) under methanogenic and sulfate-reducing conditions with an anaerobic mixed culture derived from sewage sludge. The consortium degraded PCP via 2,3,4,5-tetrachlorophenol, 3,4,5-trichlorophenol, and 3,5-dichlorophenol and eventually accumulated 3-chlorophenol. Dechlorination of PCP and metabolites was inhibited in the presence of sulfate, thiosulfate, and sulfite. A decrease in the rate of PCP transformation was noted when the endogenous dissolved H(2) was depleted below 0.11 muM in sulfate-reducing cultures. The effect on dechlorination observed with sulfate could be relieved by addition of molybdate, a competitive inhibitor of sulfate reduction. Addition of H(2) reduced the inhibition observed with sulfuroxy anions. The inhibitory effect of sulfuroxy anions may be due to a competition for H(2) between sulfate reduction and dechlorination. When cultured under methanogenic conditions, the consortium degraded several chlorinated and brominated phenols.