Studies on the response of soil microflora to the application of the fungicide fenhexamid

International audienceThe aim of this work was to evaluate the impact of the fungicide fenhexamid (FEX) on the genetic structure of soil bacterial communities using the Ribosomal Intergenic Spacer Analysis molecular technique. Using real-time PCR, we also tried to quantify the pcaH sequences which encode the dioxygenases involved in the degradation process of a variety of aromatic compounds. Soil taken from a vineyard in the Etna Park (Sicily, Italy) was treated with FEX in the ratio 2 µg g-1 soil every 7 days, the process being repeated four times. The analyses were carried out before treatment and 7 days after each further application of FEX. At the same time, the degradation rate was evaluated. The use of FEX determined a variation in the bacterial component of the soil which could be seen in an increase of some microbial strains and the inhibition of others. The pcaH sequence was already present in the genes of the soil microrganisms studied, but the use of FEX increased the number of the gene copies. These results suggest that the microbial population of the soil adapted to the presence of FEX with an increase in degradation potential. The measurements of the extent to which FEX was degraded confirm this hypothesis, showing that the molecule disappeared more quickly with successive applications

Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene

Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of tfdA in the range 1 × 10(5) to 5 × 10(7) gene copies g(−1) of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model

Evaluating the lingering effect of livestock grazing on functional potentials of microbial communities in Tibetan grassland soils

Background and aims: Livestock grazing is a widely practiced land-use regime that can impose lingering effects on global biogeochemical cycles. However, elucidating the mechanisms of related eco-processes, which are largely mediated by the microbial community, remains challenging. Methods: Here, we collected soil samples from two Tibetan grassland sites subjected to grazing in winter followed by a 3-month recovery. We then evaluated functional potentials of microbial communities via a metagenomic tool known as GeoChip 4.0. Results: Significant alterations were detected in post-grazing grassland soils, and further analysis showed that plant diversity was the best indicator of alterations in functional potentials. Relative abundances of labile C degradation genes decreased at the 3400-m site, but those of recalcitrant C degradation genes increased, which could be explained by the higher soil recalcitrant C input owing to their being substantially more forbs species at this site. Nitrification genes decreased at both sites, probably owing to increased soil moisture conducive to oxygen-limiting conditions. Relative abundance of denitrification genes increased at the 3200-m site, concomitant with increased N2O emissions. Conclusions: These results demonstrated that functional gene compositions of the microbial community were altered in post-grazing grassland soils, and linked to soil biogeochemical processes

The earthworm Aporrectodea caliginosa stimulates abundance and activity of phenoxyalkanoic acid herbicide degraders

2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid (PAA) herbicide. Earthworms represent the dominant macrofauna and enhance microbial activities in many soils. Thus, the effect of the model earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) on microbial MCPA degradation was assessed in soil columns with agricultural soil. MCPA degradation was quicker in soil with earthworms than without earthworms. Quantitative PCR was inhibition-corrected per nucleic acid extract and indicated that copy numbers of tfdA-like and cadA genes (both encoding oxygenases initiating aerobic PAA degradation) in soil with earthworms were up to three and four times higher than without earthworms, respectively. tfdA-like and 16S rRNA gene transcript copy numbers in soil with earthworms were two and six times higher than without earthworms, respectively. Most probable numbers (MPNs) of MCPA degraders approximated 4 × 105 gdw−1 in soil before incubation and in soil treated without earthworms, whereas MPNs of earthworm-treated soils were approximately 150 × higher. The aerobic capacity of soil to degrade MCPA was higher in earthworm-treated soils than in earthworm-untreated soils. Burrow walls and 0–5 cm depth bulk soil displayed higher capacities to degrade MCPA than did soil from 5–10 cm depth bulk soil, expression of tfdA-like genes in burrow walls was five times higher than in bulk soil and MCPA degraders were abundant in burrow walls (MPNs of 5 × 107 gdw−1). The collective data indicate that earthworms stimulate abundance and activity of MCPA degraders endogenous to soil by their burrowing activities and might thus be advantageous for enhancing PAA degradation in soil