Variations of Bacterial Community Structure in Flooded Paddy Soil Contaminated with Herbicide Quinclorac

The denaturing gradient gel electrophoresis (DGGE) method was applied to determine the relative genetic complexity of microbial communities in flooded paddy soil treated with herbicide quinclorac (3,7-dichloro-8-quinoline-carboylic acid). The results obtained showed a significant effect of quinclorac on the development of bacterial populations in soils contaminated with different concentrations of the herbicide at the early time after application. In general, however, the number of populations of the same soil sample treated with the same concentration of the quinclorac differed obviously with increasing incubation time within the early 8 weeks. The scale of differences in banding patterns-showed that the microbial community structures of the quinclorac-treated and non-quinclorac-treated soils were not significantly different after 21 weeks of incubation. Quantification, as demonstrated in this paper, was studied by establishing dose-response relationships. Significant pattern variations were quantified. Prominent DGGE bands were excised, cloned and sequenced to gain insight into the identities of predominant bacterial populations. The majority of DGGE band sequences were related to bacterial genera Clostridium, Sphingobacterium, Xanthomonas and Rhodococcus.     

Respiration induced by substrate and bacteria diversity after application of diuron,hexazinone, and sulfometuron-methyl alone and in mixture

Abstract

After application, herbicides often reach the soil and affect non-target soil microorganisms, decreasing their population, diversity or affecting metabolic activity. Therefore, laboratory studies were performed to evaluate the effects of diuron, hexazinone and sulfometuron-methyl alone and mixed upon carbon transformation by soil microorganisms in clayey and sandy soils and the effect on bacterial diversity and structure. Control treatment without herbicide application was also performed. Sub-samples from the control and herbicide treatments (10?g – in triplicate) were collected before herbicide application and 7, 14, 28 and 42?days after treatment (DAT), then 1?mL of ¹⁴C-glucose solution was applied. The released ¹⁴CO₂ was trapped in 2?M NaOH solution and the radioactivity was analyzed by liquid scintillation counting (LSC), 12?h after glucose application. The effect of herbicides on bacterial diversity was evaluated by T-RFLP. The experiment was conducted in a complete randomized design. Hexazinone did not affect ¹⁴CO₂ evolution. Diuron showed a greater ¹⁴CO₂ evolution in sandy and clayey soil, while sulfometuron-methyl led to an increase in sandy soil, at 42 DAT. A greater evolution of carbon was observed in the treatment with herbicide mixture in sandy soil, compared with the same treatment in clayey soil or control. However, the herbicide mixture application did not affect the soil biological activity measured by the respiration rate induced by substrate. On the other hand, the herbicide mixtures affected the bacterial diversity in both soils, being the strongest effect to diuron and sulfometuron-methyl in clayey soil and hexazinone in sandy soil.     

The effects of triclopyr on 2,4‐D mineralization in two soils

Abstract

The effects of the herbicide triclopyr (3,5,6‐trichloro‐2‐pyridinyloxyacetic acid) on the mineralization of 2,4‐D (2,4‐dichlorophenoyxacetic acid) in two soils which differed in their histories of prior exposure to the two herbicides were investigated. The relative effects of triclopyr on 2,4‐D mineralization and most probable numbers of 2,4‐D degraders were dependent upon the soil. Triclopyr was shown to increase 2,4‐D mineralization rates in a soil which had been exposed to both 2,4‐D and triclopyr, but decreased the mineralization rate of 2,4‐D and inhibited the increase of most probable numbers of 2,4‐D degraders in a soil that had not been directly exposed to either herbicide.     

Effect of green manure amendment on herbicide pendimethalin on soil

Manure amendment in agricultural practice can have a large effect on herbicide dissipation because the period of manure plowing is close to the period of herbicide application. In addition, manure amendment is among the frequently encountered options in ameliorating pesticide pollution. In this research, the dissipation of the herbicide pendimethalin was examined after amendment with two common green manures, Lupinus luteus (L) or Cosmos bipinnatus (C), for 110 days in pH 5.2 and 7.7 soils (Sankengtzu [Sk] and Erhlin [Eh] soil, respectively). The microbial activity and ecology changes were examined by using Biolog EcoPlate and denaturing gradient gel electrophoresis (DGGE). In Sk soil, the half-lives of pendimethalin with L, C, and blank treatment were 49.0, 54.9, and 62.2 days, respectively, whereas that in Eh soil they were 46.3, 52.6, and 34.8 days, respectively. Pendimethalin dissipated quickly in more neutral soil (Eh soil), but the addition of manure can only increase the dissipation rate in acidic soil (Sk soil), indicating that the amendment of manures exerted different effect in pendimethalin dissipation rates in different pH soils. The application of pendimethalin and/or manure altered the microbial community activity after 24 h of incubation. After 110 days, the microbial community activities in green manure–amended soil were more similar to that with blank than pendimethalin treatment in both types of soils. In comparison with treatment C, microbial communities were more similar between treatment L and blank, indicating the superior effect over pendimethalin on microbial communities when applying Lupinus luteus. The research showed that the application of herbicide pendimethalin changed soil microbial community, and the amendment of manures exerted different effect in pendimethalin dissipation rates in different pH soils. It is assumed that the change in dissipation rates was originated from the microbial community change after different manure amendment.     

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.     

Effects of metsulfuron‐methyl on microbial biomass and populations in soils

Abstract

Effects of the herbicide metsulfuron‐methyl on soil microorganisms and their activities in two soils were evaluated under laboratory conditions. Measurements included their populations, soil respiration, and microbial biomass. In the clay soil, bacterial populations decreased with increasing concentration of metsulfuron‐methyl during the first 9 days of incubation but exceeded that of the control soil from day 27 onward. In the sandy loam soil, the herbicide reduced bacterial populations during the first 3 days after application, but these increased to the level of untreated controls after 9 days’ incubation. Fungal populations in both soils increased with increasing metsulfuron‐methyl concentrations, especially in the sandy loam soil. CO₂ evolution was stimulated in both soils in the presence of the herbicide initially, but decreased during days 3 to 9 of the incubation period before increasing again afterward. The presence of metsulfuron‐methyl in the soil increased microbial biomass, except in sandy loam soil at the first day of incubation.     

The effect of triclosan on microbial community structure in three soils

The application of sewage sludge to land can expose soils to a range of associated chemical toxicants. In this paper we explore the effects of the broad spectrum anti-microbial compound triclosan on the phenotypic composition of the microbial communities of three soils of contrasting texture (loamy sand, sandy loam and clay) using phospholipid fatty-acid (PLFA) analysis. Each soil type was dosed and subsequently re-dosed 6 weeks later with triclosan at five nominal concentrations in microcosms (10, 100, 500, 1000 mg kg⁻¹ and a zero-dose control). PLFA profiles were analysed using multivariate statistics focussing on changes in the soil phenotypic community structure. Additionally, ratios of fungal:bacterial PLFA indicators and cyclo:mono-unsaturated PLFAs (a common stress indicator) were calculated. It was hypothesised that triclosan addition would alter the community structure in each soil with a particular effect on the fungal:bacterial ratio, since bacteria are likely to be more susceptible to triclosan than fungi. It was also hypothesised that the PLFA response to re-dosing would be suppressed due to acclimation. Although the microbial community structure changed over the course of the experiment, the response was complex. Soil type and time emerged as the most important explanatory factors. Principal component analysis was used to detect phenotypic responses to different doses of triclosan in each soil. As expected, there was a significant increase in the fungal:bacterial ratio with triclosan dose especially in treatments with the highest nominal concentrations. Furthermore, the PLFA response to re-dosing was negligible in all soils confirming the acclimation hypothesis.     

Alterations of microbial populations and composition in the rhizosphere and bulk soil as affected by residual acetochlor

Acetochlor is a widely used herbicide in maize fields; however, the ecological risk of its residue in the soil–plant system remains unknown. We investigated the dissipation dynamics of field dose acetochlor and clarified its impact on microbial biomass and community structure both in the rhizosphere and bulk soil over 1 month after its application. Soil microbial parameters such as quantities of culturable bacteria and fungi represented by colony-forming units, soil microbial biomass carbon (SMB_C), and phospholipid fatty acids (PLFAs) were determined across different sampling times. The results showed that the dissipation half-lives of acetochlor were, respectively, 2.8 and 3.4 days in the rhizosphere and bulk soil, and 0.02–0.07 μg/g residual acetochlor could be detected in the soil 40 days after its application. Compared to the bulk soil, microbial communities in the rhizosphere soil were inclined to be affected by the application of acetochlor: SMB_C content and bacterial growth were most likely to be increased; however, fungal growth was prone to be inhibited. The principal component analysis of PLFAs, as well as the comparisons of fungi/bacteria and cy17:0/C16:1ω9c ratios between different treatments over sampling time, revealed that the soil microbial community composition was significantly affected by acetochlor at its early application stage (at day 15); thereafter, the effects of acetochlor were attenuated or even could not be detected. Our results suggested that residual acetochlor did not confer a long-term impairment on viable bacterial groups in the rhizosphere and bulk soil.     

Effect of fly ash on metsulfuron-methyl sorption and leaching in soils

This investigation was undertaken to determine the effect of amendment of two fly ashes [Kota and Inderprastha (IP)] on sorption behavior of metsulfuron-methyl in three Indian soil types. Kota fly ash (5%) did not show any effect on herbicide sorption while IP fly ash significantly enhanced the sorption. Further studies on metsulfuron-methyl sorption-desorption behavior in 0.5, 1, 2, and 5% IP fly ash-amended soils suggested that effect of fly ash varied with soil type and better effect was observed in low organic carbon content soils. The sorption-desorption isotherms fitted very well to the Freundlich sorption equation and, in general, slope (1/n) values less than unity were observed. Metsulfuron-methyl sorption in the IP fly ash-amended soils showed strong correlation with the fly ash content and compared to the Freundlich sorption constant (K _f), K _FA values (sorption normalized to fly ash content) showed less variation. Metsulfuron-methyl leaching studies suggested greater retention of herbicide in the application zone in IP fly ash-amended soils, but effect varied with soil type and no herbicide leaching was observed in 5% fly ash-amended soils. The study suggested that all coal fly ashes are not effective in enhancing the sorption of metsulfuron-methyl in soils. However, one which enhanced herbicide sorption, could play an important role in reducing its leaching losses.     

Impact of the novel neonicotinoid insecticide Paichongding on bacterial communities in yellow loam and Huangshi soils

Insecticides are widely sprayed in modern agriculture for ensuring the crop yield, which could also lead to contamination and insecticide residue in soils. Paichongding (IPP) is a novel neonicotinoid insecticide and was developed recently in China. Soil bacterial community, diversity, and community composition vary widely depending on environmental factors. As for now, little is known about bacterial species thriving, bacterial community diversity, and structure in IPP-spraying soils. In present study, IPP degradation in yellow loam and Huangshi soils was investigated, and bacterial communities and diversity were examined in soil without IPP spray and with IPP spray through pyrosequencing of 16S ribosomal RNA (rRNA) gene amplicons. The degradation ratio of IPP at 60 days after treatment (DAT) reached 51.22 and 34.01 % in yellow loam and Huangshi soil, respectively. A higher richness of operational taxonomic units (OTUs) was found in yellow loam soil (867 OTUs) and Huangshi soil (762 OTUs) without IPP spray while OUTs were relatively low in IPP-spraying soils. The community composition also differed both in phyla and genus level between these two environmental conditions. Proteobacteria, Firmicutes, Planctomycetes, Chloroflexi, Armatimonadetes, and Chlorobi were stimulated to increase after IPP application, while IPP inhibited the phyla of Bacteroidetes, Actinobacteria, and Acidobacteria.     

Variations of bacterial community structure in flooded paddy soil contaminated with herbicide quinclorac

The denaturing gradient gel electrophoresis (DGGE) method was applied to determine the relative genetic complexity of microbial communities in flooded paddy soil treated with herbicide quinclorac (3,7-dichloro-8-quinoline-carboylic acid). The results obtained showed a significant effect of quinclorac on the development of bacterial populations in soils contaminated with different concentrations of the herbicide at the early time after application. In general, however, the number of populations of the same soil sample treated with the same concentration of the quinclorac differed obviously with increasing incubation time within the early 8 weeks. The scale of differences in banding patterns-showed that the microbial community structures of the quinclorac-treated and non-quinclorac-treated soils were not significantly different after 21 weeks of incubation. Quantification, as demonstrated in this paper, was studied by establishing dose-response relationships. Significant pattern variations were quantified. Prominent DGGE bands were excised, cloned and sequenced to gain insight into the identities of predominant bacterial populations. The majority of DGGE band sequences were related to bacterial genera Clostridium, Sphingobacterium, Xanthomonas and Rhodococcus.     

Effects of a sulfonylurea herbicide on the soil bacterial community

Sulfonylurea herbicides are widely used on a wide range of crops to control weeds. Chevalier® OnePass herbicide is a sulfonylurea herbicide intensively used on cereal crops in Algeria. No information is yet available about the biodegradation of this herbicide or about its effect on the bacterial community of the soil. In this study, we collected an untreated soil sample, and another sample was collected 1 month after treatment with the herbicide. Using a high-resolution melting DNA technique, we have shown that treatment with Chevalier® OnePass herbicide only slightly changed the composition of the whole bacterial community. Two hundred fifty-nine macroscopically different clones were isolated from the untreated and treated soil under both aerobic and microaerobic conditions. The strains were identified by sequencing a conserved fragment of the 16S rRNA gene. The phylogenetic trees constructed using the sequencing results confirmed that the bacterial populations were similar in the two soil samples. Species belonging to the Lysinibacillus, Bacillus, Pseudomonas, and Paenibacillus genera were the most abundant species found. Surprisingly, we found that among ten strains isolated from the treated soil, only six were resistant to the herbicide. Furthermore, bacterial overlay experiments showed that only one resistant strain (related to Stenotrophomonas maltophilia) allowed all the sensitive strains tested to grow in the presence of the herbicide. The other resistant strains allowed only certain sensitive strains to grow. On the basis of these results, we propose that there must be several biodegradation pathways for this sulfonylurea herbicide.     

Fungi in fabricated soils

Fabricated soil (FS) is usually used for landscape rehabilitation, and is an excellent example of environmental remediation. These soils were used to revitalise damaged and eroded soils caused by acid mine drainage, a common site in Western Pennsylvania. The ratio of bacterial and fungal microbiota contributes to the health, fertility and sustainability of the soil. The structure and function of the soils foodweb have been suggested for numerous times as a prime indicator of ecosystem health (Bongers, 1990; Coleman et al., 1992; Kalevitch et al., 2003). The measurement of disrupted soil processes, decreased bacterial or fungal activity or decreased fungal or bacterial biomass can indicate a problem long before the natural vegetation is lost (Bongers, 1990). After the exposure of FS to the natural habitat, we evaluated the bacterial and fungal activity in soil as this is an important indicator of soil health. Details on bacterial presence and specifics in application of FS are described in previous publications (Kalevitch et al., 2003, 2004a, 2004b). In this paper, we will concentrate on the role of fungal biomass in FS.     

2,4-Dichlorophenoxy Acetic Acid Mineralization in Amended Soil

The application of municipal biosolid or liquid hog manure to agricultural soils under laboratory conditions at 20°C influenced the fate of the herbicide 2,4-D [2,4-(dichlorophenoxy)acetic acid] in soil. When 2,4-D was added to soil at agronomic rates immediately after the addition of manure or biosolids to a coarse-textured soil, the percentage of 2,4-D mineralized at 100 days was about 47% for both treatments, compared to only 31% for control soils without amendments. The enhanced 2,4-D mineralization as a result of amendment addition was due to an increased heterotrophic microbial activity, with the greatest increases in soil respiration occurring for soils amended with biosolids. When additions of 2,4-D were delayed for one, two, or four weeks after the amendments were applied, the additions of amendments generally reduced 2,4-D mineralization in soil, particularly for manure, indicating that the effect of amendments on enhancing soil microbial activities diminished over time. In contrast, the mineralization of 2,4-D in control soils was less dependent on when 2,4-D was applied in relation to pre-incubations of soil for zero, one, two, or four weeks. The effect of manure on decreasing 2,4-D mineralization in specific soils was as large as the effect of soil texture on differences in 2,4-D mineralization across soils. Because manure was not found to impact 2,4-D sorption by soil, it is possible that 2,4-D mineralization decreased because 2,4-D transformation products were strongly sorbed onto organic carbon constituents in manure-amended soils and were therefore less accessible to microorganisms. Alternatively, microorganisms were less likely to metabolize the herbicide because they preferentially consumed the type of organic carbon in manure that is a weak sorbent for 2,4-D.     

Persistence of metsulfuron‐methyl in two soils

Abstract

The persistence of metsulfuron‐methyl in sandy loam and clay soil incubated at different temperatures and moistures contents was investigated under laboratory conditions using longbean (Vigna sesquipedalis L.) as bioassay species. A significant degradation of metsulfuron‐methyl was observed in non‐autoclaved soil rather than the autoclaved soil sample. At higher temperature, the degradation rate in non‐autoclaved soil improved with increasing soil moisture content. In non‐autoclaved sandy loam and clay soil, the half‐life was reduced from 9.0 to 5.7 and from 11.2 to 4.6 days, respectively when moisture level of sandy loam increased from 20 to 80% field capacity at 35°C. In the autoclaved soil, herbicide residue seems to have been broken down by non‐biological process. The rate of dissipation was slightly increased after the second application of the herbicide to non‐autoclaved soils but not in autoclaved soil, indicating the importance of microorganisms in the breakdown process.     

Maize,switchgrass, and ponderosa pine biochar added to soil increased herbicide sorption and decreased herbicide efficacy

Biochar, a by-product of pyrolysis made from a wide array of plant biomass when producing biofuels, is a proposed soil amendment to improve soil health. This study measured herbicide sorption and efficacy when soils were treated with low (1% w/w) or high (10% w/w) amounts of biochar manufactured from different feedstocks [maize (Zea mays) stover, switchgrass (Panicum vigatum), and ponderosa pine (Pinus ponderosa)], and treated with different post-processing techniques. Twenty-four hour batch equilibration measured sorption of ¹⁴C-labelled atrazine or 2,4-D to two soil types with and without biochar amendments. Herbicide efficacy was measured with and without biochar using speed of seed germination tests of sensitive species. Biochar amended soils sorbed more herbicide than untreated soils, with major differences due to biochar application rate but minor differences due to biochar type or post-process handling technique. Biochar presence increased the speed of seed germination compared with herbicide alone addition. These data indicate that biochar addition to soil can increase herbicide sorption and reduce efficacy. Evaluation for site-specific biochar applications may be warranted to obtain maximal benefits without compromising other agronomic practices.     

Behaviour of oxyfluorfen in soils amended with edaphic biostimulants/biofertilizers obtained from sewage sludge and chicken feathers. Effects on soil biological properties

We studied the behaviour of oxyfluorfen herbicide at a rate of 4 l ha^?1 on biological properties of a Calcaric Regosol amended with two edaphic biostimulants/biofertilizers (SS, derived from sewage sludge; and CF, derived from chicken feathers). Oxyfluorfen was surface broadcast on 11 March 2013. Two days after application of oxyfluorfen to soil, both biostimulants/biofertilizers (BS) were also applied to the soil. An unamended soil without oxyfluorfen was used as control. For 2, 4, 7, 9, 20, 30, 60, 90 and 120 days of the application of herbicide to the soil and for each treatment, the soil dehydrogenase, urease, β-glucosidase and phosphatase activities were measured. For 2, 7, 30 and 120 days of the application of herbicide to the soil and for each treatment, soil microbial community was determined. The application of both BS to soil without the herbicide increased the enzymatic activities and soil biodiversity, mainly at 7 days of beginning the experiment. However, this stimulation was higher in the soil amended with SS than for CF. The application of herbicide in organic-amended soils decreased the inhibition of soil enzymatic activities and soil biodiversity. Possibly, the low-molecular-weight protein content easily assimilated by soil microorganisms is responsible for less inhibition of these soil biological properties.     

Isolation and characterization of mesotrione-degrading Bacillus sp. from soil

Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-Dôme, France) showed that the soil microflora were able to biotransform it.Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods.Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it.     

Effect of selected herbicides on activities of microorganisms in soils

Abstract

With the exception of EPTC, herbicide treatments showed inhibitory effects on bacterial colony counts in a sandy loam soil for the first week. Monolinuron and simazine were stimulatory to the growth of fungi in the organic soil after 2 wk. None of the herbicide treatments affected nitrification during the first week of incubation. Except the treatment of EPTC in organic soil, all herbicides inhibited nitrification after 2 wk in both soils. All herbicide treatments stimulated SO₄ formation during the 8‐wk period in the sandy loam soil. Simazine and tridiphane also stimulated sulfur oxidation after 4 wk in an organic soil. With the exception of EPTC and nitrapyrin, no significant inhibitory effect on the amount of biomass‐C was observed in the organic soil. A stimulatory effect on denitrification was observed with EPTC for 2 wk and monolinuron for 1 wk in the sandy loam soil and with simazine and tridiphane after 2 wk in the organic soil. It is apparent that the indigenous soil microorganisms can tolerate the effects of the chemicals for control of soil weeds.