Relative effect of glyphosate on glyphosate-tolerant maize rhizobacterial communities is not altered by soil properties

The rhizobacterial composition varies according to the soil properties. To test if the effect of herbicides on the rhizobacterial communities of genetically modified NK603 glyphosate-tolerant maize varies according to different soil locations, a comparison was made between the effects of glyphosate (Roundup Plus), a post-emergence applied herbicide, and a pre-emergence applied herbicide (GTZ) versus untreated soil. The potential effect was monitored by direct amplification, cloning, and sequencing of the soil DNA encoding 16S rRNA, and high-throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region. The results obtained using three different methods to analyze the herbicide effect on the rhizobacterial communities of genetically modified NK603 maize were comparable to those previously obtained when glyphosate-tolerant maize was grown in soil with different characteristics. Both herbicides decreased the bacterial diversity in the rhizosphere, with Actinobacteria being the taxonomic group most affected. The results suggest that both herbicides affected the structure of the maize rhizobacterial community, but glyphosate was environmentally less aggressive.     

Potential accumulative effect of the herbicide glyphosate on glyphosate-tolerant maize rhizobacterial communities over a three-year cultivation period

Background

Glyphosate is a herbicide that is liable to be used in the extensive cultivation of glyphosate-tolerant cultivars. The potential accumulation of the relative effect of glyphosate on the rhizobacterial communities of glyphosate-tolerant maize has been monitored over a period of three years.

Methodology/Principal Findings

The composition of rhizobacterial communities is known to vary with soil texture, hence, the analyses have been performed in two agricultural fields with a different soil texture. The accumulative effects of glyphosate have been monitored by means of high throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from rhizobacterial communities. The relative composition of the rhizobacterial communities does vary in each field over the three-year period. The overall distribution of the bacterial phyla seems to change from one year to the next similarly in the untreated and glyphosate-treated soils in both fields. The two methods used to estimate bacterial diversity offered consistent results and are equally suitable for diversity assessment.

Conclusions/Significance

The glyphosate treatment during the three-year period of seasonal cultivation in two different fields did not seem to significantly change the maize rhizobacterial communities when compared to those of the untreated soil. This may be particularly relevant with respect to a potential authorisation to cultivate glyphosate-tolerant maize in the European Union.     

Effects of glufosinate‐ammonium herbicide and pod sealant on spider Pardosa agrestis

Herbicides based upon glufosinate‐ammonium (GLA) are among the world's most widely used. They also are applied on the most prominent oil crops as desiccants in combination with pod sealants to prevent pod shatter and seed loss close to harvest. Even though these crops occupy a significant part of the world's agroecosystems, the effects of GLA herbicides on non‐target arthropods, and in particular natural enemies of pests, have been studied very rarely, and such effects of pod sealants have never been studied. We studied in our laboratory mortality as well as prey capture efficiency of the common GLA herbicide and desiccant Basta 15^®, pod sealant Arrest^®, and a mixture of both on the wolf spider Pardosa agrestis. We found that Basta 15^® and the mixture had lethal effect on spiders. We also found significant, short‐term effect on predatory activity of spiders after all treatments. Basta 15^® significantly influenced the amount of captured prey also in the long term. This is the first study showing lethal effect on spiders of the herbicide and herbicide plus pod sealant mixture. This is also the first study examining the effects of pod sealant on the mortality and predatory activity of a pest antagonist. More studies regarding the effects of agricultural chemical mixes are needed to uncover their effects on beneficial organisms existing within agroecosystems.     

Low concentrations of glyphosate‐based herbicide cause complete loss of sperm motility of yellowtail tetra fish Astyanax lacustris

Environmental relevant concentrations of glyphosate‐based herbicide as 50 µg l^?1, 300 µg l^?1 and 1800 µg l^?1 can affect sperm quality of yellowtail tetra fish Astyanax lacustris . Viability of sperm cells was impaired at 300 µg l^?1, a concentration that is within legal limits in U.S.A. waterbodies, while motility was impaired at 50 µg l^?1, which is the more stringent limit set in Brazilian law. Therefore, environment protection agencies must review regulations of glyphosate‐based herbicides on water bodies.     

Comparison of DNA‐ and RNA‐based bacterial community structures in soil exposed to 2,4‐dichlorophenol

Aims: To examine the effect of the pollutant 2,4‐dichlorophenol on DNA‐ and RNA‐based bacterial communities in soil. Methods and Results: Soil was exposed to 100 mg kg^?1 of 2,4‐dichlorophenol (2,4‐DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T‐RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse‐transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned. Conclusions: A significant difference between active (RNA‐based) and total (DNA‐based) bacterial community structure was observed for both T‐RFLP and phylogenetic analyses in response to 2,4‐DCP, with more pronounced changes seen in RNA‐based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles. Significance and Impact of the Study: This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4‐DCP, and highlights the importance of including RNA‐based 16S rRNA analysis to complement any molecular study in a perturbed soil.     

Effect of nitrogen and phosphorus fertilization on the composition of rhizobacterial communities of two Chilean Andisol pastures

The effect of nitrogen (N) and phosphorus (P) fertilization on composition of rhizobacterial communities of volcanic soils (Andisols) from southern Chile at molecular level is poorly understood. This paper investigates the composition of rhizobacterial communities of two Andisols under pasture after 1- and 6-year applications of N (urea) and P (triple superphosphate). Soil samples were collected from two previously established sites and the composition of rhizobacterial communities was determined by denaturing gradient gel electrophoresis (PCR–DGGE). The difference in the composition and diversity between rhizobacterial communities was assessed by nonmetric multidimensional scaling (MDS) analysis and the Shannon–Wiener index. In Site 1 (fertilized for 1 year), PCR–DGGE targeting 16S rRNA genes and MDS analysis showed that moderate N application (270 kg N ha^?1 year^?1) without P significantly changed the composition of rhizobacterial communities. However, no significant community changes were observed with P (240 kg P ha^?1 year^?1) and N–P application (270 kg N ha^?1 year^?1 plus 240 kg P ha^?1 year^?1). In Site 2 (fertilized for 6 years with P; 400 kg P ha^?1 year^?1), PCR–DGGE targeting rpoB, nifH, amoA and alkaline phosphatase genes and MDS analysis showed changes in rhizobacterial communities only at the highest rate of N application (600 kg N ha^?1 year^?1). Quantitative PCR targeting 16S rRNA genes also showed higher abundance of bacteria at higher N application. In samples from both sites, the Shannon–Wiener index did not show significant difference in the diversity of rhizobacterial communities. The changes observed in rhizobacterial communities coincide in N fertilized pastures with lower soil pH and higher pasture yields. This study indicates that N–P application affects the soil bacterial populations at molecular level and needs to be considered when developing fertilizer practices for Chilean pastoral Andisols.     

Effect of Cry1Ab protein on rhizobacterial communities of Bt-maize over a four-year cultivation period

Background

Bt-maize is a transgenic variety of maize expressing the Cry toxin from Bacillus turingiensis. The potential accumulation of the relative effect of the transgenic modification and the cry toxin on the rhizobacterial communities of Bt-maize has been monitored over a period of four years.

Methodology/Principal Findings

The accumulative effects of the cultivation of this transgenic plant have been monitored by means of high throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region from rhizobacterial communities. The obtained sequences were subjected to taxonomic, phylogenetic and taxonomic-independent diversity studies. The results obtained were consistent, indicating that variations detected in the rhizobacterial community structure were possibly due to climatic factors rather than to the presence of the Bt-gene. No variations were observed in the diversity estimates between non-Bt and Bt-maize.

Conclusions/Significance

The cultivation of Bt-maize during the four-year period did not change the maize rhizobacterial communities when compared to those of the non-Bt maize. This is the first study to be conducted with Bt-maize during such a long cultivation period and the first evaluation of rhizobacterial communities to be performed in this transgenic plant using Next Generation Sequencing.     

Diversity of 16S rRNA and dioxygenase genes detected in coal‐tar‐contaminated site undergoing active bioremediation

Aims: In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation‐independent communities is available. Methods and Results: Coal‐tar‐contaminated soil was collected, which consisted of 122·5 mg g^?1 total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal‐tar‐contaminated soil, targeting the 16S rRNA to characterize (i) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center (α‐subunit) common to all PAH dioxygenase enzymes and (iii) β‐subunit of dioxygenase. Phylotypes related to Proteobacteria (Alpha‐, Epsilon‐ and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of α‐subunit and β‐subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type [2Fe‐2S] cluster binding site suggested that these gene fragments encode for α‐subunit of dioxygenase gene. Conclusions: Sequencing of the cloned libraries representing α‐subunit gene fragments (Rf1) and β‐subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal‐tar‐contaminated soil. Significance and Impact of the Study: The combination of the Rieske primers and bacterial community profiling represents a powerful tool for both assessing bioremediation potential and the exploration of novel dioxygenase genes in a contaminated environment.     

A Sensitive Method to Monitor <Emphasis Type="Italic">Bacillus subtilis</Emphasis> and <Emphasis Type="Italic">Streptomyces coelicor</Emphasis>-related Bacteria in Maize Rhizobacterial Communities: The Use of Genome-Wide Microarrays

Commercially available DNA microarrays containing genome-wide spotted oligonucleotides encompass the soil bacteria Bacillus subtilis or Streptomyces coelicolor genomes. These have been used to analyse potential differences in rhizobacterial communities of transgenic maize engineered to express the Bacillus thuringensis Cry toxin (Bt maize) in three different agricultural soils. No differences in hybridisation were observed between genetically and non-genetically modified maize rhizobacteria from two Bt lines with a detection sensitivity of five copies of a particular gene above the background. Soil-specific hybridisation results were obtained when rhizobacterial DNA was compared to the corresponding genomic DNA spotted in the microarrays suggesting that the use of genome-wide DNA arrays could serve as a useful tool for the molecular monitoring of rhizobacterial communities. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Residual herbicide treatments reduce Andropogon gayanus (Gamba Grass) recruitment for mine site restoration in northern Australia

Weed invasion is a major threat to Australian tropical savannas, and controlling weeds is essential for successful re‐establishment of native species on disturbed sites. Gamba Grass (Andropogon gayanus) is an African grass which has invaded large areas of tropical savanna across northern Australia. Current management strategies in northern Australia focus on fire and glyphosate to effectively control mature plants; however, re‐establishment of infestations from the soil seed bank remains a major challenge to eradication efforts. This study focused on the effects of soil seed bank treatments on Gamba Grass recruitment on a mine site in northern Australia. Adult Gamba Grass plants within test plots were killed with glyphosate to exclude resource competition. Chemical, physical and biological treatments were then applied, and the treatment effects on subsequent Gamba Grass seedling emergence and survival quantified. Seedling emergence was significantly reduced by three of the four residual herbicide treatments tested. The most effective herbicide treatments, dalapon and sulfometuron, reduced emergence by 90% compared to the standard glyphosate treatment alone. This equated to a reduction in Gamba Grass seedling emergence from 1 seedling/m² to 1 seedling 10 m^?2, a major improvement for Gamba Grass management. These residual herbicide treatments significantly reduced the population density of Gamba Grass for at least 5 months after emergence. The physical and biological treatments did not have a significant effect on seedling emergence. This significant reduction in Gamba Grass seedling emergence and survival can substantially improve Gamba Grass management. Reducing re‐colonisation from the soil seed bank using residual herbicides provides a valuable management tool for land managers, integrating readily with established strategies for controlling the mature plants.     

Aldo‐keto reductase enzymes detoxify glyphosate and improve herbicide resistance in plants

In recent years, concerns about the use of glyphosate‐resistant crops have increased because of glyphosate residual levels in plants and development of herbicide‐resistant weeds. In spite of identifying glyphosate‐detoxifying genes from microorganisms, the plant mechanism to detoxify glyphosate has not been studied. We characterized an aldo‐keto reductase gene from Pseudomonas (PsAKR1) and rice (OsAKR1) and showed, by docking studies, both PsAKR1 and OsAKR1 can efficiently bind to glyphosate. Silencing AKR1 homologues in rice and Nicotiana benthamiana or mutation of AKR1 in yeast and Arabidopsis showed increased sensitivity to glyphosate. External application of AKR proteins rescued glyphosate‐mediated cucumber seedling growth inhibition. Regeneration of tobacco transgenic lines expressing PsAKR1 or OsAKRI on glyphosate suggests that AKR can be used as selectable marker to develop transgenic crops. PsAKR1‐ or OsAKRI‐expressing tobacco and rice transgenic plants showed improved tolerance to glyphosate with reduced accumulation of shikimic acid without affecting the normal photosynthetic rates. These results suggested that AKR1 when overexpressed detoxifies glyphosate in planta.     

The absorption, translocation and distribution of the herbicide glyphosate in maize expressing the CP-4 transgene

Maize (Zea mays L. var. Bonnie) transformed with a gene encoding a 5-enolpyruvylshikimate 3-phosphate synthase with altered sensitivity showed over 100-fold greater resistance to the herbicide glyphosate (N-[phosphonomethyl]glycine) in comparison with its non-transformed progenitor (parental control) at the third-leaf stage. Studies with [¹⁴C]-glyphosate at a dosage lethal to the parental control, but sublethal to the transgenic, revealed that a maximum of 45-65% of the applied dose was absorbed, with greater absorption occurring in transgenic plants. Translocation of glyphosate was closely related to its absorption (r value 0.956) with approximately 15% more of the applied dose being mobilized in transgenic plants than the parental controls. Analysis of electronic autoradiograms along the treated leaf lamina found discrete internal regions of glyphosate accumulation closely associated with the site of application. These regions contained lower amounts of glyphosate present in the treated leaf lamina was almost completely translocated in transgenic plants, while in the parental controls more remained and the leaf became necrotic. In both types of maize there was a small accumulation of herbicide in the tip region of the leaf which was not mobilized. Younger shoot tissues and roots were major sinks for translocated glyphosate accumulating approximately 25-40% of the applied dose depending upon treatment. In the parental control, equal amounts of glyphosate were found distributed between young shoot tissues and roots; while in transgenic plants, the young shoot tissue accumulated around three times more glyphosate than the roots. In both plant types, glyphosate was localized in the meristems and young, actively growing leaves. Specific glyphosate activity (the amount of glyphosate per unit dry weight of tissue) in the major sinks of the transgenic declined towards the end of the treatment period but remained relatively constant in the parental control. In conclusion, enhancing glyphosate resistance by genetic transformation influenced the absorption, translocation and distribution of this herbicide in whole plants.Keywords: Zea mays, glyphosate (N-[phosphonomethyl]-glycine), transgenic, absorption, translocation, source-sink.      

No evidence for early fitness penalty in glyphosate‐resistant biotypes of Conyza canadensis: Common garden experiments in the absence of glyphosate

Strong selection from herbicides has led to the rapid evolution of herbicide‐resistant weeds, greatly complicating weed management efforts worldwide. In particular, overreliance on glyphosate, the active ingredient in RoundUp^®, has spurred the evolution of resistance to this herbicide in ≥40 species. Previously, we reported that Conyza canadensis (horseweed) has evolved extreme resistance to glyphosate, surviving at 40× the original 1× effective dosage. Here, we tested for underlying fitness effects of glyphosate resistance to better understand whether resistance could persist indefinitely in this self‐pollinating, annual weed. We sampled seeds from a single maternal plant (“biotype”) at each of 26 horseweed populations in Iowa, representing nine susceptible biotypes (S), eight with low‐level resistance (LR), and nine with extreme resistance (ER). In 2016 and 2017, we compared early growth rates and bolting dates of these biotypes in common garden experiments at two sites near Ames, Iowa. Nested ANOVAs showed that, as a group, ER biotypes attained similar or larger rosette size after 6 weeks compared to S or LR biotypes, which were similar to each other in size. Also, ER biotypes bolted 1–2 weeks earlier than S or LR biotypes. These fitness‐related traits also varied among biotypes within the same resistance category, and time to bolting was inversely correlated with rosette size across all biotypes. Disease symptoms affected 40% of all plants in 2016 and 78% in 2017, so we did not attempt to measure lifetime fecundity. In both years, the frequency of disease symptoms was greatest in S biotypes and similar in LR versus ER biotypes. Overall, our findings indicate there are no early growth penalty and possibly no lifetime fitness penalty associated with glyphosate resistance, including extremely strong resistance. We conclude that glyphosate resistance is likely to persist in horseweed populations, with or without continued selection pressure from exposure to glyphosate.     

Responses of invertebrates to herbicide in Salix cinerea invaded wetlands: Restoration implications

The use of herbicides to control weeds, particularly large invasions, has now become an essential management tool in many ecological restoration projects. The herbicide glyphosate is routinely used to control the invasive weed, Grey Willow (Salix cinerea), within New Zealand wetlands. However, little is known about the effects of glyphosate on invertebrates. We determine the short‐term effects of glyphosate on the abundance and composition of the nontarget canopy invertebrate community in wetlands invaded by Grey Willow in New Zealand. Initially, the application of glyphosate and a surfactant showed no detectable effect on the canopy invertebrates examined in this study. However, 27 days after herbicide application, significant Grey Willow canopy loss caused dramatic decreases in the abundance of invertebrates in the glyphosate‐treated plots compared with the unsprayed plots. Invertebrates appeared to be sensitive to changes in vegetation structure, such as canopy loss. These results agree with previous studies that have shown that the negative impacts of glyphosate on invertebrate communities are related to indirect effects via habitat modification as the herbicide‐treated vegetation dies. From a terrestrial invertebrate perspective, this study suggests that the use of glyphosate herbicide is suitable for the control of invasive weeds within wetland restoration projects as it appears to have negligible impact on the canopy invertebrate assemblage.     

A preliminary assessment of the response of a native reptile assemblage to spot‐spraying invasive Bitou Bush with glyphosate herbicide

During recent work examining the effects of Bitou Bush (Chrysanthemoides monilifera ssp. rotundata) invasion on native reptile assemblages in coastal heathland vegetation in Eastern Australia, unplanned spot‐spraying of glyphosate occurred at some of our experimental sites invaded by Bitou Bush. We used this unexpected herbicide application as an opportunity to provide a preliminary assessment of the short‐term impacts on reptiles of glyphosate spot‐spraying of Bitou Bush. Using an M‐BARCI design, we compared reptile assemblages among uninvaded (reference) sites, invaded (control) sites and invaded and sprayed (impact) sites before and after spraying. We found no significant short‐term (7 – 10 months) differences in reptile abundance, species richness or assemblage composition among invaded, uninvaded and sprayed sites before and after glyphosate application. We cautiously interpret our results to generate a preliminary finding that spot‐spraying of Bitou Bush with glyphosate appears not to have a deleterious effect on reptile assemblages at seven and ten months following herbicide application. While we would not recommend basing management decisions on the outcomes of our study alone, we suggest that our findings can be used to assist in the development of strategic analyses of glyphosate impacts on native flora and fauna.     

Inoculation with the Plant-Growth-Promoting Rhizobacterium Azospirillum brasilense Causes Little Disturbance in the Rhizosphere and Rhizoplane of Maize (Zea mays)

Inoculation with Azospirillum brasilense exerts beneficial effects on plant growth and crop yields. In this study, a comparative analysis of maize (Zea mays) root inoculated or not inoculated with A. brasilense strains was performed in two soils. Colonization dynamics of the rhizobacteria were tracked in various root compartments using 16S rRNA-targeted probes and 4′,6′diamidino-2-phenylindole staining, and the structure of bacterial populations in the same samples was analyzed by denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction products of the 16S rRNA gene. Based on whole cell hybridization, a large fraction of the bacterial community was found to be active in both the rhizoplane–endorhizosphere and rhizosphere soil compartments, in both soil types. A DGGE fingerprint analysis revealed that plant inoculation with A. brasilense had no effect on the structural composition of the bacterial communities, which were also found to be very similar at the root tip and at zones of root branching. However, rhizobacterial populations were strongly influenced by plant age, and their complexity decreased in the rhizoplane–endorhizosphere in comparison to rhizosphere soil. A clone library generated from rhizosphere DNA revealed a highly diverse community of soil and rhizosphere bacteria, including an indigenous Azospirillum-like organism. A large proportion of these clones was only distantly related to known species. Herschkovitz and Lerner contributed equally to this work.     

Meta‐barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

This study was designed to assess the influence of three soil DNA extraction procedures, namely the International Organization for Standardization (ISO‐11063, GnS‐GII and modified ISO procedure (ISOm), on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico‐chemical characteristics and land use. A meta‐barcoded pyrosequencing approach targeting 16S and 18S rRNA genes was applied to characterize soil microbial communities. We first observed that the GnS‐GII introduced some heterogeneity in bacterial composition between replicates. Then, although no major difference was observed between extraction procedures for soil bacterial diversity, we saw that the number of fungal genera could be underestimated by the ISO‐11063. In particular, this procedure underestimated the detection in several soils of the genera Cryptococcus, Pseudallescheria, Hypocrea and Plectosphaerella, which are of ecological interest. Based on these results, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities. Indeed, the ISOm procedure provides a better evaluation of bacterial and fungal communities and is limited to the modification of the mechanical lysis step of the existing ISO‐11063 standard.     

Novel α‐ketoglutarate dioxygenase tfdA‐related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides

Phenoxyalkanoic herbicides such as 2,4‐dichlorophenoxyacetate (2,4‐D), 2,4‐dichlorophenoxybutyrate (2,4‐DB) or mecoprop are widely used to control broad‐leaf weeds. Several bacteria have been reported to degrade these herbicides using the α‐ketoglutarate‐dependent, 2,4‐dichlorophenoxyacetate dioxygenase encoded by the tfdA gene, as the enzyme catalysing the first step in the catabolic pathway. The effects of exposure to different phenoxyalkanoic herbicides in the soil bacterial community and in the tfdA genes diversity were assessed using an agricultural soil exposed to these anthropogenic compounds. Total community bacterial DNA was analysed by terminal restriction fragment length polymorphism of the 16S rRNA and the tfdA gene markers, and detection and cloning of tfdA gene related sequences, using PCR primer pairs. After up to 4 months of herbicide exposure, significant changes in the bacterial community structure were detected in soil microcosms treated with mecoprop, 2,4‐DB and a mixture of both plus 2,4‐D. An impressive variety of novel tfdA gene related sequences were found in these soil microcosms, which cluster in new tfdA gene related sequence groups, unequally abundant depending on the specific herbicide used in soil treatment. Structural analysis of the putative protein products showed small but significant amino acid differences. These tfdA gene sequence variants are, probably, required for degradation of natural substrate(s) structurally related to these herbicides and their presence explains self‐remediation of soils exposed to phenoxyalkanoic herbicides.     

Role of eukaryotic microbiota in soil survival and catabolic performance of the 2,4-D herbicide degrading bacteria <Emphasis Type="Italic">Cupriavidus necator</Emphasis> JMP134

Cupriavidus necator (formerly Ralstonia eutropha) JMP134, harbouring the catabolic plasmid pJP4, is the best-studied 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide degrading bacterium. A study of the survival and catabolic performance of strain JMP134 in agricultural soil microcosms exposed to high levels of 2,4-D was carried out. When C. necator JMP134 was introduced into soil microcosms, the rate of 2,4-D removal increased only slightly. This correlated with the poor survival of the strain, as judged by 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) profiles, and the semi-quantitative detection of the pJP4-borne tfdA gene sequence, encoding the first step in 2,4-D degradation. After 3 days of incubation in irradiated soil microcosms, the survival of strain JMP134 dramatically improved and the herbicide was completely removed. The introduction of strain JMP134 into native soil microcosms did not produce detectable changes in the structure of the bacterial community, as judged by 16S rRNA gene T-RFLP profiles, but provoked a transient increase of signals putatively corresponding to protozoa, as indicated by 18S rRNA gene T-RFLP profiling. Accordingly, a ciliate able to feed on C.␣necator JMP134 could be isolated after soil enrichment. In␣native soil microcosms, C. necator JMP134 survived better than Escherichia coli DH5α (pJP4) and similarly to Pseudomonas putida KT2442 (pJP4), indicating that species specific factors control the survival of strains harbouring pJP4. The addition of cycloheximide to soil microcosms strongly improved survival of these three strains, indicating that the eukaryotic microbiota has a strong negative effect in bioaugmentation with catabolic bacteria.