Microbial degradation of penoxsulam in flooded rice field soils

The degradation of penoxsulam [2-(2,2-difluoroethoxy)-N-5,8-dimethoxy[1,2,4]triazolo[1,5-C]pyrimidin-2-yl-6-(trifluoromethyl)benzene-sulfonamide] was studied in flasks simulating flooded rice field conditions using four representative rice field soils from the Sacramento Valley. Degradation half-lives (t(1/2) values) ranged between 2 and 13 days. Increased degradation rates were observed in flask systems with steeper redox gradients between the flooded soil layer and the overlaying water. Two transient metabolites were identified that were temporarily formed in amounts exceeding 5% of the total initial mass of penoxsulam. The results of high-performance liquid chromatography/(14)C radiodetection studies indicate that the degradation of the triazolopyrimidine system and its substituents is the main pathway of microbial transformation processes. Microbial activity, as measured by dehydrogenase activity, was not affected by penoxsulam concentrations corresponding to the proposed maximum annual use rate of 40 g active ingredient/ha.     

Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

By using cultivation-independent techniques, community changes of methane-oxidizing bacteria (MOB) in rice bulk soils were investigated under field conditions in a Japanese rice field. The representative soil samples were collected during the typical rice growing season and nonrice growing period all year round. Statistical characterization of denaturing gradient gel electrophoresis (DGGE) community patterns of MOB pmoA/amoA functional gene fragments showed that MOB community structures in the rice bulk soils remained largely unchanged throughout the investigated period. The total intensity of six common DGGE bands that appeared consistently throughout the investigated period accounted for 64% of the total intensity of all 18 different DGGE bands detected. The low squared distance of the Ward cluster analysis of the DGGE pattern and the high Sorensen similarity coefficient (81%) also implied the high similarity of the MOB community structures. The stable MOB community structure did not couple well with the wide variation of soil water contents all year round. Sequencing analysis of the nine characteristic bands including six common bands revealed the presence of Type I, Type II methanotrophs, and β-proteobacterial ammonia oxidizers in rice bulk soils. In comparison with MOB type species, three DGGE bands showed a wide variation of the highly conserved amino acid residues, implying the presence of novel MOB bacteria inhabiting the rice bulk soil. The high diversity of MOB composition suggested that rice bulk soils might serve as an ideal reservoir for the dynamic changes of MOB in a rice field ecosystem in response to environment changes.     

Modeling within field variation of the compaction layer in a paddy rice field using a proximal soil sensing system

A key characteristic of flooded paddy fields is the plough pan. This is a sub‐soil layer of greater compaction and bulk density, which restricts water losses through percolation. However, the thickness of this compacted layer can be inconsistent, with consequences such as variable percolation and leaching losses of nutrients, which therefore requires precision management of soil water. Our objective was to evaluate a methodology to model the thickness of the compacted soil layer using a non‐invasive electromagnetic induction sensor (EM38‐MK2). A 2.7 ha alluvial non‐saline paddy rice field was measured with a proximal soil sensing system using the EM38‐MK2 and the apparent electrical conductivity (EC_a) of the wet paddy soil was recorded at a high‐resolution (1.0 × 0.5 m). Soil bulk density (n = 10) was measured using undisturbed soil cores, which covered locations with large and small EC_a values. At the same locations (within 1 m²) the depth of the different soil layers was determined by penetrometer. Then a fitting procedure was used to model the EC_a – depth response functions of the EM38‐MK2, which involved solving a system of non‐linear equations and a R² value of 0.89 was found. These predictions were evaluated using independent observations (n = 18) where a Pearson correlation coefficient of 0.87 with an RMSEE value of 0.03 m was found. The EC_a measurements allowed the detail estimation of the compacted layer thickness. The link between water percolation losses and thickness of the compacted layer was confirmed by independent observations with an inverse relationship having a Pearson correlation coefficient of 0.89. This rapid, non‐invasive and cost‐effective technique offers new opportunities to measure differences in the thickness of compacted layers in water‐saturated soils. This has potential for site‐specific soil management in paddy rice fields.     

Toxicity of Uranium to Microbial Communities in Anaerobic Biofilms

Microbial processes have shown promise for the remediation of uranium and nitrate in groundwater impacted by uranium mine tailings. This study investigated the inhibitory impact of uranium(VI) towards different microbial populations in anaerobic biofilms, including methanogenic, denitrifying, and uranium-reducing microorganisms, which are commonly found at uranium bioremediation sites. Results of batch activity bioassays indicated a very distinct level of toxicity depending on the targeted microbial community. U(VI) caused severe inhibition of acetoclastic methanogenesis as indicated by a 50?% inhibiting concentration (IC₅₀) of only 0.16?mM. Denitrifying populations were also impacted by uranium, but their sensitivity depended on the electron donor utilized. Sulfur-oxidizing denitrifiers were the least affected (IC₅₀ for denitrification activity?=?0.32?mM), followed by H₂- and acetate-utilizing denitrifiers (IC₅₀ of 0.20 and 0.15?mM, respectively). In contrast, exposure to U(VI) concentrations up to 1.0?mM did not inhibit the rate of U(VI) bioreduction with H₂ as electron donor in the presence or absence of nitrate. On the contrary, a considerable increase in the uranium-reducing activity of the denitrifying and methanogenic mixed cultures was observed with increasing uranium concentrations. The results suggest that microorganisms responsible for U(V) reduction could tolerate much higher uranium concentrations compared to the other microbial populations assayed.     

Microbial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field determined by phospholipid fatty acid (PLFA) analysis

To identify the microbial communities responsible for the decomposition of rice straw compost in soil during the rice cultivation period, phospholipid fatty acid (PLFA) composition of rice straw compost was determined by periodically sampling the compost from a Japanese rice field under flooded conditions. About 21% of the compost was decomposed within a period of 3 months. The total amount of PLFAs, as an indicator of microbial biomass, was significantly lower under drained conditions than under flooded conditions and was relatively constant during the flooding period. This indicates that the microbial biomass in the compost samples did not increase during the gradual decomposition of rice straw compost under flooded conditions. The proportion of branched-chain PLFAs (biomarker of Grampositive and anaerobic Gram-negative bacteria) slightly decreased during the early period after placement, and increased gradually afterwards. Among the branched-chain PLFAs, i15:0, ail5:0, i16:0 and i17:0 PLFAs predominated and their proportions increased gradually except for i16:0. The proportion of straight mono-unsaturated PLFAs (biomarker of Gramnegative bacteria) was almost constant throughout the period, and 18:1ω9 and 18:1ω7 PLFAs predominated. The proportion of straight poly-unsaturated PLFAs as a biomarker of eukaryotes including fungi was also constant throughout the period, except for a decrease under drained conditions. Straight poly-unsaturated PLFAs consisted mainly of 18:2ω6c PLFA. Therefore, these results suggest that the proportions of Gram-positive and anaerobic Gram-negative bacteria increased during the decomposition of rice straw compost in flooded paddy field. Statistical analyses enabled to divide PLFA patterns of microbiota in the rice straw compost into two groups, one group consisting of rice straw compost samples collected before mid-season drainage and the other of samples collected after mid-season drainage. Small squared distances among samples in cluster analysis indicated that the community structure of microbiota was similar to each other as a whole. These results suggest that the microbial communities changed gradually during the period of placement, and that mid-season drainage may have affected the community structure of microbiota. Principal component analysis of the PLFA composition suggested that the succession of microbiota along with the decomposition in flooded soil was similar between rice straw compost and rice straw and that the changes in the community structure during the decomposition in flooded soil were more conspicuous for rice straw than for rice straw compost.     

Degradation of estrogenic hormones in a silt loam soil

Estrogenic hormones are endocrine-disrupting compounds, which disrupt the endocrine system function of animals and humans by mimicking and/or antagonizing endogenous hormones. With the application of sludge biosolid and animal manure as alternative fertilizers in agricultural lands, estrogens enter the soil and become an environmental concern. The degradation kinetics of 17beta-estradiol, an estrogenic hormone of major concern, in a silt loam soil were investigated in this study. It was found that 17beta-estradiol degraded rapidly in nonsterilized soil with a half-life of 0.17 day. The degradation rate constant was proportional to the percentage of nonsterilized soil, indicating that microorganisms are directly responsible for the rapid degradation of 17beta-estradiol in soil. The half-life of 17beta-estradiol in 20% nonsterilized soil was slightly shortened from 1.3 to 0.69 day with the increase of soil moisture from 10 to 20% and was greatly decreased from 4.9 to 0.92 day with the increase of temperature from 15 to 25 degrees C. The coexistence of 40 micromol kg (-1) sulfadimethoxine, a veterinary antibiotic, decreased the degradation rate constant of 17beta-estradiol from 0.750 +/- 0.038 to 0.492 +/- 0.016 day (-1). The degradation kinetics of another three estrogenic hormones, including 17alpha-estradiol, estrone, and estriol, were also investigated and compared. Estrone was identified as a degradation product of 17beta-estradiol and the most persistent hormone among the four investigated estrogens. Estriol was observed in the degradation of estrone and 17alpha-estradiol.     

Microbial community responsible for the decomposition of rice straw in a paddy field: estimation by phospholipid fatty acid analysis

To estimate the microbial communities responsible for rice straw decomposition in paddy field, phospholipid fatty acid (PLFA) composition of leaf sheaths and blades was analyzed during the decomposition of both residues under upland conditions after harvest and under flooded conditions at the time of transplanting of rice plants. In addition, rice straw that had been placed in the field under upland conditions (November to April) was taken out in spring, and placed again in the same field under flooded conditions at the time of transplanting. High proportions of the branched-chain PLFAs were observed under flooded conditions (June to September); the proportions of straight mono-unsaturated and straight poly-unsaturated PLFAs were high under upland conditions in the winter season for 4 months. The dominant PLFAs in straight mono-unsaturated, straight poly-unsaturated and branched-chain PLFA groups were 18:19, 18:17 and 16:17c, 18:26c and i15:0, i17:0 and ai15:0, respectively, under both upland and flooded conditions. These findings indicated the important roles of Gram-negative bacteria and fungi under upland conditions and of Gram-positive bacteria and anaerobic Gram-negative bacteria under flooded conditions. Cluster analysis of PLFA composition showed the difference of community structure of microbiota in rice straw between upland and flooded conditions. In addition principal component analysis revealed the difference between leaf sheaths and blades under upland conditions and indicated that the content of straight unsaturated PLFAs (sheaths > blades) characterized their community structures.     

Microbial Degradation of Fipronil in Clay Loam Soil

Fipronil, (±)-5-amino-1-(2,6-dichloro-∝,∝,∝-trifluoro-p-tolyl)-4-trifluoromethysulfinylpyrazole-3-carbonitrile, is used as an effective insecticide for the control of rice pests in China. Although many studies examining the fate of fipronil in the soilenvironment have been conducted, there are no studies on the microbial degradation of fipronil in the soil environment. Fipronil was degradedby microorganisms in the non-sterile clay loam soil, which resulted in the formation of metabolite, MB45950. The degradation of fipronil in non-sterile clay loam soil was mainly influenced by the soil microbes. The half-lives in non-sterile clay loam soil were 9.72 and 8.78 d at 25 and 35 °C, respectively compared to 33.51 and 32.07 d at 25 and 35 °C, respectively in the sterile soil. The microbial viability test showed that non-sterile clay loam soil had viable microorganisms throughout the experiment. Fipronil did not adversely affect the microbes once soil microbes adapted to the presence of fipronil in the clay loam soil.     

Persistence of hexachlorocyclohexane isomers in soil planted with rice and in rice rhizosphere soil suspensions

Summary The relative persistence of -, and -isomers of hexachlorocyclohexane (HCH) was studied in a flooded soil with and without rice seedlings under greenhouse conditions. -HCH was more stable than - and -HCH in both planted and unplanted systems. - and -HCH decreased to negligible levels (5.5% for the -isomer and 2.4% for the -isomer) after 30 days in planted and unplanted soils. During the same period, 30.9% of the added -HCH was recovered from planted soil and 50.6% from unplanted soil. Likewise, in anaerobically (H₂ + CO₂ atmosphere) incubated mineral salts solution inoculated with suspensions from rice rhizosphere and non-rhizosphere soils, -HCH decreased to low levels (< 15%) within 5 days. Most of the added -HCH was recovered from mineral solution inoculated with nonrhizosphere soil suspension even after 30 days while -HCH decreased to 53.6% of the original level in mineral solution inoculated with rice rhizosphere soil suspension. The data reveal that the degradation of anaerobically unstable HCH isomers is not retarded by the possible aeration of a flooded soil by rice roots.     

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.     

A phototrophy-driven microbial food web in a rice soil

Purpose  

Light is a major driver of primary productivity in most ecosystems on Earth. Phototrophic microorganisms harvest light to synthesize organic biomass for sustaining the global energy and carbon flow. However, the bottom-up model of phototrophic microorganisms as primary production and food source for higher trophic levels remains unclear in the terrestrial environment.     

Microbial activity affected by lime in a long-term no-till soil

Under conventional farming practices, lime is usually applied on the soil surface and then incorporated into the soil to correct soil acidity. In no-till (NT) systems, where lime is surface applied or only incorporated into the soil to very shallow depth, lime will likely not move to where it is required within reasonable time. Consequently, lime may have to be incorporated into the soil by mechanical means. The objective of this laboratory study was to characterize the effect of lime, incorporated to different depths, on chemical and biological soil properties in a long-term NT soil. Soil samples taken from the 0–5, 0–10, and 0–20 cm depths were analyzed in incubation studies for soil pH, nitrate, CO₂ respiration, and microbial biomass-C (MBC). Lime (CaCO₃) was applied at rates equivalent to 0, 4.4, 8.8, and 17.6 Mg ha⁻¹. Application of lime to both 0–10 and 0–20 cm depths increased soil pH from about 4.9 by 1, 1.7, and 2.8 units for the low, medium, and high liming rates, respectively. Soil nitrate increased over time and in proportion to liming rate, suggesting that conditions were favorable for N-mineralization and nitrification. Greater respiration rates and greater MBC found in lime-treated than in non-limed soils were attributed to higher soil pH. Faster turnover rates and increased mineralization of organic matter were found in lime-treated than in non-limed soils. These studies show that below-surface lime placement is effective for correcting soil acidity under NT and that microbial activity and nitrification can be enhanced.     

Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

Wild rice (Oryza rufipogon) is a problematic weed in fields of cultivated rice (Oryza sativa). We hypothesized that the composition and/or the activity of the methanogenic microbial communities might be different in soil grown with cultivated versus wild rice. We used samples from Hainan, China, where wild rice grew on a field adjacent to cultivated rice. The composition of the methanogenic archaeal community was analyzed in samples of rice soil by targeting the 16S rRNA gene. Analysis of the terminal restriction fragment length polymorphism (T-RFLP) showed similar patterns in soil from wild versus cultivated rice. Sequences of archaeal 16S rRNA genes also showed similar composition in soil from wild versus cultivated rice, revealing the presence of Methanosarcinaceae, Methanosaetaceae, Methanobacteriales, Methanocellales (Rice Cluster I), Rice Cluster II, Crenarchaeota Group I.3 and Crenarchaeota Group I.1b. Incubation of soil samples under anoxic conditions generally resulted in vigorous CH₄ production after a lag phase of 7-8 days. Production of CH₄ was partially inhibited by methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, resulting in nearly stoichiometric accumulation of acetate. CO₂ was produced without lag phase. The δ¹³C of the produced CO₂ was slightly lower in soil grown with cultivated rice versus wild rice, reflecting the δ¹³C of organic matter, which was about −29‰ for cultivated rice soil and about −24‰ for wild rice soil. The δ¹³C of the produced CH₄ and the acetate that accumulated in the presence of CH₃F was much more negative in cultivated versus wild rice soil, mainly since the isotopic fractionation factors for hydrogenotrophic methanogenesis were higher for soil from cultivated rice (α = 1.054) versus wild rice (α = 1.039). However, the percentage contribution of hydrogenotrophic methanogenesis to total CH₄ production was similar in both soils (27-35%). In conclusion, although the two soils exhibited different δ¹³C values of soil organic matter and derived products, they were similar with respect to rates and composition of the methanogenic communities.     

Chlorothalonil Degradation under Anaerobic Conditions in an Agricultural Tropical Soil

Chlorothalonil, a halogenated benzonitrile compound, is one of the most widely used fungicides in the world. Anaerobic microcosm assays were established to evaluate the combined effect of the initial content of carbon (6.3, 9.45 and 12.6 mg g^-1), nitrogen (0.6, 1.8 and 3 mg g^-1)and chlorothalonil (432, 865 and 1298 ηg g^-1) on the biodegradation of this fungicide by microbiota from an agricultural tropical soil. A Box-Behnken experimental design was used and chlorothalonil depletion was followed by HPLC with UV detection. The initial carbon content and fungicide dose were found to have a significant effect on removal efficiency. After 25 days of incubation, a high chlorothalonil depletion was observed in all biologically active microcosms (56–95%) although abiotic loss in a sterile blank was also notable (37%). The results suggest a high potential for chlorothalonil biodegradation under anaerobic conditions by indigenous microbial communities from soil that has been continuously exposed to high doses of the fungicide.     

Degradation and adsorption of fosthiazate in soil

Adsorption and degradation behavior of a pesticide in soil has a strong effect on its environmental fate as well as efficacy for pest control. Fosthiazate is an organophosphate compound that is currently under development as a nonfumigant nematicide. In this study, we evaluated adsorption and degradation kinetics of fosthiazate in three U.S. soils with different properties. Adsorption of fosthiazate in mineral soil was negligibly weak but appeared to increase with soil organic matter (OM) content. The half-life (T(1/2)) of fosthiazate ranged from 0.5 to 1.5 months in nonsterile soils but was prolonged to 1-3 months after sterilization. Degradation of fosthiazate in soil appeared to be caused by both chemical and microbial transformations. The persistence of fosthiazate generally decreased with increasing soil pH, but increased with increasing soil OM and clay contents. This results suggest that fosthiazate may have an enhanced leaching potential in acidic soils with low OM content, and its efficacy in high pH soils may not last as long as in neutral soils because of faster degradation.     

Effect of temperature on the rate limiting step in the methanogenic degradation pathway in rice field soil

Temperature is an important factor controlling CH₄ production in rice field soils. However, it is unknown which step in the methanogenic degradation of organic matter is the limiting one that is controlled by temperature. Soil slurries prepared from Italian rice field soil were anaerobically incubated in the dark at six different temperatures between 10 and 37 °C until quasi-steady state was reached. Then, the potential and actual rates of polysaccharide hydrolysis and of CH₄ production from different immediate (acetate, H₂) and distal (glucose, propionate) methanogenic substrates were determined. Potential activities of exo-glucanase and glucosidase were always higher than the actual rates of polysaccharide hydrolysis indicating that the availability of the polysaccharide substrate was limiting at all temperatures. The actual rates of CH₄ production were always lower than those predicted from glucose release during polysaccharide hydrolysis indicating that a substantial amount of the released glucose was assimilated into microbial biomass. Addition of the different methanogenic substrates stimulated CH₄ production at all temperatures >10 °C, but only at >20 °C to values higher than rates of polysaccharide hydrolysis. Under steady state conditions, however, hydrolysis of organic polymers was the rate-limiting step at all temperatures >10 °C.     

Microbial performance under increasing nitrogen availability in a Mediterranean forest soil

In forest ecosystems, the external nitrogen (N) inputs mainly involve wet and dry depositions that potentially alter inorganic N availability in the soil and carbon (C) turnover. This study assesses the effect of a slow increase of inorganic N availability on microbial community activity and functionality in a Mediterranean forest soil. A four-month incubation experiment was performed with soil collected from the organic layer of a forest site and fertilized with a solution of ammonium nitrate. The fertilizer was supplied at an equivalent of 0, 10, 25, 50 and 75 kg N ha⁻¹ (0, 0.3, 0.7, 1.3 and 2 mg N g⁻¹ for control N0 and treatments N1, N2, N3 and N4, respectively). The incubation was carried out under optimal conditions, with the addition of the nutritive solution in small aliquots once a week to mimic the phenomenon of N deposition. In order to isolate the effect of N, the pH of the NH₄NO₃ solutions was adjusted to soil pH, and phosphorus was added in order to prevent any nutrient limitation effect. Inorganic N, C-mineralization, the activity of one oxidative enzyme (o-diphenol oxidase) and 8 hydrolitic enzymes (α-glucosidase, β-glucosidase, N-acetyl-β-d-glucosaminidase, cellulase, leucine amino-peptidase, acid phosphatase, butyric esterase and β-xylosidase) and the community level physiological profile (CLPP) were measured and analyzed during the whole incubation and at the end of the experiment as a proxy for microbial decomposition activity. In the first month, the highest N availability (N4) repressed the microbial respiration activity but stimulated microbial enzymatic activity, suggesting a change of C-pathways from spilling to enzymes and biomass investment. The treatments N1, N2 and N3 had no effect in the same period. Throughout the incubation, a general stress condition affected all the treated soils. As a consequence, treated soils exhibited higher respiration rates than the control. This was accompanied by a loss of functional diversity and an end-detected decline in biomass C. Although at the end of incubation most of the soil features showed a clear correlation with the inorganic N pool, the organic C content was strongly affected by different patterns of microbial activity during the experiment: the highest N treatment (N4) showed a lower C loss than the N3 treatment. Overall, the experiment showed how inorganic N availability can potentially alter the C cycle in a Mediterranean forest soil. The effect is non linear, depending on microbial community dynamics, on the community’s ability to adapt given the time scale of the process, and on N supply amount. Our study also revealed a common pattern in the short-term response to N addition in other, similar ecosystems with different climatic conditions.     

Degradation of Sevin by soil microorganisms

Microorganisms capable of transforming the pesticide 1-naphthyl N-methyl-carbamate (Sevin) were isolated from soil. Three isolates were able to accelerate the hydrolysis of Sevin to 1-naphthol. Several unidentified intermediates were separated by thin-layer chromatography and also by following the decomposition of Sevin-methyl-¹⁴C. Since 1-naphthol is a biological as well as a chemical decomposition product of Sevin, its transformation by the isolated microbes was also studied. A fungus, identified as Fusarium solani, altered 1-naphthol rapidly. Whereas one strain of bacterium degraded the hydrolysis product gradually, another strain accumulated it under certain conditions. Mixed cultures of the investigated microbes were more effective in transforming Sevin than pure cultures, and this phenomenon was also observed with 1-naphthol as substrate with the exception of one bacterial strain.