Soil microbial activities in a constructed soil reed-bed under cheese-dairy farm effluents

Soil microbial activities in a reed-bed used for effluent purification of a small cheese-dairy farm under a Mediterranean climate were described and studied. This work aims to demonstrate (i) whether certain enzyme activities used as bioindicators of dairy waste degradation (beta-galactosidase and protease) vary over time, which might influence organic matter degradation and (ii) whether specific microbial communities are selected through contact with the discarded effluent using community level catabolic profiles (CLCPs). beta-galactosidase and protease activities were followed in a 14-month monitoring experiment. These enzyme activities were strongly expressed during the whey-discarding period from February to May. CLCPs using Biolog Ecoplate showed great microbial diversity, as described by Shannon-Weaver index, and no difference was observed in microbial diversity between areas at the receiving end of the reed-bed (where effluent was discarded) and those at the opposite end. This may be explained by successive environmental factors which made enzyme activities vary: whey discarded from February to May and Mediterranean climate conditions (drying-rewetting effects on summer). Microbial enumeration using epifluorescence microscopy also showed a pattern linked to Mediterranean conditions with a drastic decrease in biomass during summer drought. These results on functional biodiversity were correlated with high purification yields: the minimum decrease in Biological Demand in Oxygen was 84% and that in suspended solids was 75%.     

The effects of pesticides on bacterial nitrogen fixers in peanut-growing area

In the peanut production, the applications of herbicides and fungicides are a common practice. In this work, studies done under field conditions demonstrated that pesticides affected negatively the number and nitrogenase activity of diazotrophic populations of soil. Agrochemical effects were not transient, since these parameters were not recovered to pre-treatment levels even 1 year after pesticides application. Results obtained from greenhouse experiments revealed that the addition of herbicide or fungicides diminished the free-living diazotrophs number reaching levels found in soil amended with the pesticides and that the number of symbiotic diazotrophs was not affected by the insecticide assayed. The soil nitrogenase activity was not affected by fungicides and glyphosate. The effect of pesticides on the nitrogen-fixing bacteria diversity was evaluated both in field and greenhouse experiments. Analysis of clone libraries generated from the amplification of soil nifH gene showed a diminution in the genetic diversity of this bacterial community.     

Stability of bacterial populations in tropical soil upon exposure to Lindane

The effect of the pesticide Lindane on microbial populations was analyzed in soil with a history of contamination with various chemicals, including this pesticide. Soil microcosms were amended with 100 mg Lindane/kg soil and microbial populations were monitored for 70 days. Bacterial cell concentrations, metabolic versatility (whole community Biolog), and genetic diversity (16S rDNA/denaturing gradient gel electrophoresis) were used to monitor microbial communities. Results show the persistence of Lindane in the soil environment; at the end of the experiment, 70% of the added Lindane remained undegraded. A reduction of 50% in bacterial cell concentration was observed in Lindane-amended microcosms during the 2nd week of the experiment. This reduction was correlated with a reduction in the rate of substrate utilization as observed by Biolog. Overall, no effect of Lindane was observed on the metabolic versatility and genetic diversity in these soils, demonstrating the ability of these bacterial populations to tolerate the pressure caused by the addition of pesticides.     

Effects of the Inoculant Strain Sphingomonas paucimobilis 20006FA on Soil Bacterial Community and Biodegradation in Phenanthrene-contaminated Soil

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO₂ production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.     

Polyvinyl alcohol biodegradation under denitrifying conditions

Polyvinyl alcohol was biodegraded under denitrifying conditions with a microbial community originated from a municipal wastewater treatment plant. The derived microbial consortium was capable of polyvinyl alcohol degradation under both denitrifying and aerobic conditions. The community dynamics was monitored by temperature gradient gel electrophoresis, and a principal utilizing organism was identified and assigned as Steroidobacter sp. PD. The possible role of Steroidobacter sp. PD was also investigated by sequencing the 16S rDNA clone library prepared from the degrading community. qPCR analysis showed that the fraction of the microorganism in the community was very low initially (0.02%) and had reached to about 16% by the end of the biodegradation experiment. The study revealed that polyvinyl alcohol can be biodegraded in a water environment not only under aerobic but also under denitrifying conditions.     

Do Botanical Pesticides Alter the Structure of the Soil Microbial Community?

The effects of synthetic pesticides on the soil microbial community have been thoroughly investigated in the past mostly by culture-dependent methods and only few recent studies have used culture-independent approaches for this purpose. However, it should be noted that most of these studies have been conducted in microcosms where the soil microbial community is exposed to unrealistic concentrations of the pesticides, providing an unrealistic exposure scheme for soil microorganism. On the other hand, little is known regarding the potential impact of botanical pesticides on the soil microbial community. Therefore, a laboratory study and a field study were conducted to investigate the effects of synthetic (metham sodium [MS], sodium tetrathiocarbonate [SoTe], and fosthiazate) and botanical pesticides (azadirachtin, quillaja, and pulverized Melia azedarach fruits [PMF]) on the soil microbial community using phospholipid fatty acids (PLFA) analysis. Principal component analysis (PCA) on the results of the laboratory study indicated that the application of PMF resulted in significant changes in the soil microbial community. This was obvious by the proportional increase in the abundance of fatty acids 18:1ω9cis, 18:1ω9trans, which are common in gram-negative bacteria and saprotrophic fungi, and 18:2ω6,9, which is a fungal indicator. This response was attributed to the release of copious amounts of organic carbon and nutrients in the soil by the PMF. On the other hand, MS inhibited fungi and gram-negative bacteria, while fosthiazate and the botanical pesticides quillaja and azadirachtin did not impose significant changes in the soil microbial community. Similar results were obtained by the field study where application of the fumigants MS and SoTe significantly altered the structure of the soil microbial community with the former having a more prominent effect. Fosthiazate imposed mild changes in the soil microbial community, whereas quillaja and azadirachtin again did not show a significant effect. Overall, botanical pesticides, at their recommended dose, did not alter the structure of the soil microbial community compared to synthetic nonfumigant and fumigant pesticides which induced significant changes.     

杀虫剂类POPs对土壤中微生物群落多样性的影响

农药类持久性有机污染物(POPs)如DDT和HCH在我国2 0世纪5 0年代到80年代曾广泛使用,在停止使用2 0 a后,在土壤中仍然可以检测到DDT和HCH的残留。利用BIOL OG微平板研究土壤微生物群落功能多样性,意在反映有机氯杀虫剂类POPs对土壤微生物群落多样性的影响。结果表明,加了HCH后土壤微生物群落的颜色平均变化值(AWCD)的变化速度和最终能达到的AWCD值要高于空白土壤,并且随着农药浓度的加大,AWCD值的变化速率也越来越快,最终能达到的最大值也呈比例增大。加了DDT后的土壤与空白土壤的AWCD变化速度和程度相差不大。方差分析结果表明:空白土壤、HCH0 .5mg/kg、HCH1.5 mg/kg各处理间土壤的AWCD值有显著性差异(p<0 .0 1) ,空白土壤、DDT0 .5 m g/kg、DDT1.5 m g/kg各处理间土壤的AWCD值达不到显著性差异的水平(p>0 .0 5 ) ,表层土壤的AWCD值要高于第2层土壤(p<0 .0 1)。从多样性指数的变化来看,当加入到土壤中的DDT和HCH含量稍低时,微生物会利用农药为碳源进行分解作用,从而刺激了微生物的生长,这时表现出丰富度、均匀性和多样性都呈增长趋势。但当农药的浓度进一步加大时,反而会抑制某些种的微生物生长,另外一些种则对加入到土壤中的农药有一定的耐受性,从而表现出群落的均匀性下降,而丰富度升高。在相同施用浓     

Molecular identification of the microbial diversity in two sequencing batch reactors with activated sludge

The diversity of the microbial community was identified in two lab-scale, ideally mixed sequencing batch reactors which were run for 115 days. One of the reactors was intermittently aerated (2 h aerobically/2 h anaerobically) whereas the other was consistently aerated. The amount of biomass as dry matter, the degradation of organic carbon determined by chemical oxygen demand and nitrogen-degradation activity were followed over the operation of the two reactors and did not show significant differences between the two approaches at the end of the experiment. At this point, the composition of the microbial community was determined by a terminal restriction fragment length polymorphism approach using multiple restriction enzymes by which organisms were retrieved to the lowest taxonomic level. The microbial composition was then significantly different. The species richness was at least five-fold higher in the intermittently aerated reactor than in the permanently kept aerobic approach which is in line with the observation that ecosystem disturbances result in higher diversity.     

Using volatile organic compounds to enhance atrazine biodegradation in a biobed system

The effect of the terpenes α-pinene, eucalyptol, and limonene, individually and as mixtures, on atrazine (ATZ) biodegradation and on biological activity in a biobed biomixture was evaluated. Additionally, terpenes emitted from the biomixture were captured using solid-phase microextraction. Terpenes added individually at relatively low concentrations (50 μg kg^?1) significantly enhanced ATZ degradation and biological activity during the first incubation days. No significant effect on ATZ degradation was found from adding the terpene mixture, and, interestingly, an inhibitory effect on phenoloxidase activity was found during the first 20 days of incubation when mixed terpenes were present at 100 μg kg^?1. Capturing terpenes demonstrated that during the first hour of incubation a significant fraction of the terpenes was volatilized. These results are the first to demonstrate the feasibility of using terpenes to enhance the degradation of a pesticide. However, successive applications of terpenes or the addition of materials that slowly release terpenes could sustain the ATZ degradation enhancement.     

The effect of Saccharomyces cerevisiae on concentration of dicarboxymide and acylanilide fungicides and pyrethroid insecticides during fermentation

Summary Continuing the investigation into possible yeast influence on ferment degradation of residual pesticides, two dicarboxymide antibotrytic fungicides (Iprodione and Procymidone), three acylanilide antiperonosporic fungicides (Benalaxyl, Furalaxyl and Ofurace) and two pyrethroid insecticides (Permethrin and Fenvalerate) were tested.Only the pyrethroids were degraded completely during fermentation.     

Drawing-up of pesticide selectivity lists to beneficial arthropods for IPM programmes in potato

In order to promote IPM programmes in potato, the toxicity of 19 fungicides, 4 herbicides and 11 insecticides commonly used in this crop in Belgium was assessed on three beneficial arthropods. These species were representative of the most important aphid specific natural enemies encountered in potatoes: a parasitic wasp--Aphidius rhopalosiphi (De Stefani-Perez) (Hym., Aphidiidae), a ladybird--Adalia bipunctata (L.) (Col., Coccinellidae) and a hoverfly--Episyrphus balteatus (Dipt., Syrphidae). In a first time, pesticides were tested on glass plates on A. rhopalosiphi adults and A. bipunctata and E. balteatus larvae. For each insect, products inducing corrected mortality (Mc) lower than 30% were directly classified in a positive list for harmless products (green list). The other compounds were further tested on plants and listed in toxicity classes according to mortalities induced during this extended laboratory test: harmless (Mc < 30%), slightly harmful (30% < Mc < 60%), moderately harmful (60% < Mc < 80%) and harmful (Mc > 80). A chemical determination of pesticides residues was also performed for each experiment in order to determine the exposure of beneficial arthropods to pesticide residues and to validate the application of chemicals on tested substrates. On the basis of the results of acute toxicity tests, the period of each pesticide use according to normal agricultural practices and the abundance and importance of the three different groups of aphid natural enemies at different periods of the year, four pesticides lists were built up. Each list corresponded to a different period of pesticides application: Period I--from seedling to beginning of June (based on A. rhopalosiphi tests), Period II--beginning to end of June (based on A. rhopalosiphi tests), Period III beginning to end of July (based on E. balteatus and A. bipunctata tests) and Period IV--August to harvest (no exposure of beneficials). Results showed that herbicides were not toxic to the three species and can be used according to normal agricultural practices without restrictions. All fungicides can also be used without restrictions at recommended rates. Only the mixture Metalaxyl-M + Fluazinam was slightly harmful to A. bipunctata but had no effects on A. rhopalosiphi and E. balteatus. Results were more contrasted for insecticides and none of them was totally selective for all the 3 beneficial arthropods. Therefore, they can only be used with restrictions at periods II and III, according to the beneficial species that need to be protected.     

Labile and Recalcitrant Organic Matter Utilization by River Biofilm Under Increasing Water Temperature

Microbial biofilms in rivers contribute to the decomposition of the available organic matter which typically shows changes in composition and bioavailability due to their origin, seasonality, and watershed characteristics. In the context of global warming, enhanced biofilm organic matter decomposition would be expected but this effect could be specific when either a labile or a recalcitrant organic matter source would be available. A laboratory experiment was performed to mimic the effect of the predicted increase in river water temperature (+4?°C above an ambient temperature) on the microbial biofilm under differential organic matter sources. The biofilm microbial community responded to higher water temperature by increasing bacterial cell number, respiratory activity (electron transport system) and microbial extracellular enzymes (extracellular enzyme activity). At higher temperature, the phenol oxidase enzyme explained a large fraction of respiratory activity variation suggesting an enhanced microbial use of degradation products from humic substances. The decomposition of hemicellulose (β-xylosidase activity) seemed to be also favored by warmer conditions. However, at ambient temperature, the enzymes highly responsible for respiration activity variation were β-glucosidase and leu-aminopeptidase, suggesting an enhanced microbial use of polysaccharides and peptides degradation products. The addition of labile dissolved organic carbon (DOC; dipeptide plus cellobiose) caused a further augmentation of heterotrophic biomass and respiratory activity. The changes in the fluorescence index and the ratio Abs(250)/total DOC indicated that higher temperature accelerated the rates of DOC degradation. The experiment showed that the more bioavailable organic matter was rapidly cycled irrespective of higher temperature while degradation of recalcitrant substances was enhanced by warming. Thus, pulses of carbon at higher water temperature might have consequences for DOC processing.     

History matters: Heterotrophic microbial community structure and function adapt to multiple stressors

Ecosystem functions in streams (e.g., microbially mediated leaf litter breakdown) are threatened globally by the predicted agricultural intensification and its expansion into pristine areas, which is associated with increasing use of fertilizers and pesticides. However, the ecological consequences may depend on the disturbance history of microbial communities. To test this, we assessed the effects of fungicides and nutrients (four levels each) on the structural and functional resilience of leaf‐associated microbial communities with differing disturbance histories (pristine vs. previously disturbed) in a 2 × 4 × 4‐factorial design (n = 6) over 21 days. Microbial leaf breakdown was assessed as a functional variable, whereas structural changes were characterized by the fungal community composition, species richness, biomass, and other factors. Leaf breakdown by the pristine microbial community was reduced by up to 30% upon fungicide exposure compared with controls, whereas the previously disturbed microbial community increased leaf breakdown by up to 85%. This significant difference in the functional response increased in magnitude with increasing nutrient concentrations. A pollution‐induced community tolerance in the previously disturbed microbial community, which was dominated by a few species with high breakdown efficacies, may explain the maintained function under stress. Hence, the global pressure on pristine ecosystems by agricultural expansion is expected to cause a modification in the structure and function of heterotrophic microbial communities, with microbially mediated leaf litter breakdown likely becoming more stable over time as a consequence of fungal community adaptions.     

Effects of salinity on microbial tolerance to drying and rewetting

Soil salinity and fluctuations in soil matric potential are stressors for soil microorganisms which, in turn, may affect soil organic matter turnover. In response to salinity and low soil water content, many microorganisms accumulate osmolytes. Therefore, it is conceivable that microorganisms in saline soils are more tolerant to drying and rewetting (DRW) stress than those in non-saline soils. An experiment was carried out with three different salinity levels: electrical conductivity (EC_1:5) 0, 2 and 4 dS m^?1 (EC0, EC2, EC4), and two water treatments: a constantly moist control or two DRW cycles. Respiration as an indicator of microbial activity was measured throughout the 59 days of incubation. At the end of the second dry period (day 35) and at the end of the following moist incubation (day 59), microbial biomass and microbial community structure were determined by phospholipid fatty acid (PLFA) analysis. Increasing salinity decreased microbial activity but did not affect its resistance to DRW. On day 59, cumulative respiration decreased in the order EC0 > EC2 > EC4 with no differences between water treatments. Fungal biomass was negatively affected by salinity at the end of the experiment, while bacterial biomass was unaffected. Microbial community structure in moist treatments differed between salinity levels, with EC4 influencing microbial community structure earlier than EC2. The resistance of microbial communities to DRW stress was salt level dependent; only beyond a critical salinity level adaptation to salt stress was able to reduce the impact of water stress on microbial community structure.     

Associated impact of inorganic fertilizers and pesticides on microbial communities in soils

This study was designed to examine the reaction of microbial communities to the associated impact of inorganic fertilizers and pesticides during laboratorial simulation for 90 days. Soils were sampled from fields in three different stations of Chinese Ecosystem Research Network (CERN). The metabolic profiles were characterized by using BIOLOG GN2 microplates. The Shannon Index (H) showed that the metabolic diversity of the three types of soil exhibited similar profiles. PCA and CLUSTER further explored the variance in community structures with the same H. There were obvious changes in the structures of microbial communities during the 90-day duration of the work and the three different types of soil showed␣similar profiles for most of the period of the experiment.     

Pesticide dissipation and microbial community changes in a biopurification system: influence of the rhizosphere

The dissipation of atrazine, chlorpyrifos and iprodione in a biopurification system and changes in the microbial and some biological parameters influenced by the rhizosphere of Lolium perenne were studied in a column system packed with an organic biomixture. Three column depths were analyzed for residual pesticides, peroxidase, fluorescein diacetate activity and microbial communities. Fungal colonization was analyzed by confocal laser scanning microscopy to assess the extent of its proliferation in wheat straw. The L. perenne rhizosphere enhanced pesticide dissipation and negligible pesticide residues were detected at 20–30 cm column depth. Atrazine, chlorpyrifos and iprodione removal was 82, 89 and 74% respectively in the first 10 cm depth for columns with vegetal cover. The presence of L. perenne in contaminated columns stimulated peroxidase activity in all three column depth sections. Fluorescein diacetate activity decreased over time in all column sections with the highest values in biomixtures with vegetal cover. Microbial communities, analyzed by PCR-DGGE, were not affected by the pesticide mixture application, presenting high values of similarity (>65%) with and without vegetal cover. Microbial abundance of Actinobacteria varied according to treatment and no clear link was observed. However, bacterial abundance increased over time and was similar with and without vegetal cover. On the other hand, fungal abundance decreased in all sections of columns after 40 days, but an increase was observed in response to pesticide application. Fungal colonization and straw degradation during pesticide dissipation were verified by monitoring the lignin autofluorescence loss.     

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure

The effect of veterinary antibiotics in anaerobic digesters is a concern where methane production efficiency is highly dependent on microbial community structure. In this study, both anaerobic degradation of a common veterinary antibiotic, oxytetracycline (OTC), and its effects on an anaerobic digester microbial community were investigated. Qualitative and quantitative molecular tools were used to monitor changes in microbial community structure during a 60-day batch incubation period of cow manure with the addition of different concentrations of the antibiotic. Molecular data were interpreted by a further redundancy analysis as a multivariate statistics approach. At the end of the experiment, approximately 48, 33, and 17 % of the initially added 50, 100, and 200 mg l^?1 of OTC was still present in the serum bottles which reduced the biogas production via accumulation of some of the volatile fatty acids (VFAs). Biogas production was highly correlated with Methanobacteriales and Methanosarcinales gene copy numbers, and those parameters were negatively affected with oxytetracycline and VFA concentrations.     

Fatty Acid Methyl Ester (FAME) Succession in Different Substrates as Affected by the Co-Application of Three Pesticides

Introduction

In intensive agriculture areas the use of pesticides can alter soil properties and microbial community structure with the risk of reducing soil quality.

Materials and Methods

In this study the fatty acid methyl esters (FAMEs) evolution has been studied in a factorial lab experiment combining five substrates (a soil, two aged composts and their mixtures) treated with a co-application of three pesticides (azoxystrobin, chlorotoluron and epoxiconazole), with two extraction methods, and two incubation times (0 and 58 days). FAMEs extraction followed the microbial identification system (MIDI) and ester-linked method (EL).

Results and Discussion

The pesticides showed high persistence, as revealed by half-life (t_1/2) values ranging from 168 to 298 days, which confirms their recalcitrance to degradation. However, t_1/2 values were affected by substrate and compost age down to 8 days for chlorotoluron in S and up to 453 days for epoxiconazole in 12M. Fifty-six FAMEs were detected. Analysis of variance (ANOVA) showed that the EL method detected a higher number of FAMEs and unique FAMEs than the MIDI one, whereas principal component analysis (PCA) highlighted that the monosaturated 18:1ω9c and cyclopropane 19:0ω10c/19ω6 were the most significant FAMEs grouping by extraction method. The cyclopropyl to monoenoic acids ratio evidenced higher stress conditions when pesticides were applied to compost and compost+soil than solely soil, as well as with final time.

Conclusion

Overall, FAMEs profiles showed the importance of the extraction method for both substrate and incubation time, the t_1/2 values highlighted the effectiveness of solely soil and the less mature compost in reducing the persistence of pesticides.     

Biomonitoring of continuous microbial community adaptation towards more efficient phenol-degradation in a fed-batch bioreactor

The anaerobic degradation of phenol was studied in a fed-batch culture. Nitrate was added as electron acceptor and phenol was provided three times, to a final concentration of 200 mg/l. Randomly amplified polymorphic DNA (RAPD) and terminal fraction fragment length polymorphism (T-RFLP) were used and compared in order to monitor the microbial succession in the reactor. Phenol degradation started after an initial lag phase of 14 days and was then completed within a few days. In addition, the duration of the lag phase was shortened and the degradation rate was increased after each phenol amendment. Nitrate reduction correlated with microbial growth and phenol depletion, confirming that the degradation was carried out anaerobically. Results from the DNA analysis showed that the structure of the microbial community changed after each phenol amendment. This study confirms the potential for anaerobic degradation of environmental pollutants and also confirms that microbial acclimation towards faster degradation rates occurred upon repeated substrate amendments. Furthermore, both of the DNA-based techniques described the phenol degradation-linked community shifts with similar general results. RAPD is a faster, simpler technique that gives a higher resolution and consequently reflects the shifts in the microbial community structure better, whereas T-RFLP is more suitable for phylogenetic studies.