Role of eukaryotic microbiota in soil survival and catabolic performance of the 2,4-D herbicide degrading bacteria Cupriavidus necator JMP134

Abstract

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 DH5alpha (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.

Bioaugmentation with Pseudomonas sp. strain MHP41 promotes simazine attenuation and bacterial community changes in agricultural soils

“…Abiotic factors such as pH, extremes in temperature, water content and nutrient availability may influence the survival of introduced microorganisms. In addition, predation and competition by indigenous microbiota could decrease the added organisms (Bouchez et al , 2000; Gentry et al , 2004; Thompson et al , 2005; Manzano et al , 2007). In this report the effectiveness of Pseudomonas sp.…”

Degradation of trace concentrations of the persistent groundwater pollutant 2,6-dichlorobenzamide (BAM) in bioaugmented rapid sand filters

“…However, as MSH1-bacteria were also eventually lost from the filter operated without backwashing, other factors such as protozoan grazing and bacterial starvation are likely to contribute to the loss. Protozoan predation has been shown to significantly reduce bioaugmentation efficiency in contaminated aquifer sediments (Cunningham et al, 2009;Kota et al, 1999), in a nitrifying batch reactor (Bouchez et al, 2000) and in soil (Manzano et al, 2007). However, the effect of protozoan grazing on bioaugmentation of waterworks sand filters has not been investigated previously.…”

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

“…The striking aspect of the findings reported here is that these novel tfdA genes related sequences are detected in only one soil. This soil has been subjected to standard farming practices with annual weed control based on the use of s ‐triazine herbicides such as simazine and, quite occasionally, with MCPA herbicide to control simazine resistant weeds (Manzano et al ., 2007). The presence of these numerous tfdA gene related sequences may explain the rapid turnover of 2,4‐D in this soil (Manzano et al ., 2007).…”

“…This soil has been subjected to standard farming practices with annual weed control based on the use of s ‐triazine herbicides such as simazine and, quite occasionally, with MCPA herbicide to control simazine resistant weeds (Manzano et al ., 2007). The presence of these numerous tfdA gene related sequences may explain the rapid turnover of 2,4‐D in this soil (Manzano et al ., 2007). Their detection in non‐incubated soil and in soil microcosms exposed to benzoic acid or water indicates that these tfdA genes related sequences are abundant enough to be detected in the soil total genomic DNA without a need for enrichment of the bacteria harbouring gene sequences putatively involved in degradation of specific PA herbicides.…”

“…Soil total genomic DNA was isolated from 1 g soil samples at the beginning of the experiment and after 4 months using the ‘Ultra Clean Soil DNA Kit’ (MoBio Laboratories), following the instructions of the manufacturers, and modifications reported elsewhere (Manzano et al ., 2007).…”