Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere.

Methanol, the second most abundant volatile organic compound, primarily released from plants, is a major culprit disturbing atmospheric chemistry. Interestingly, ubiquitously found methanol-utilizing bacteria, play a vital role in mitigating atmospheric methanol effects. Despite being extensively characterized, the effect of nitrogen sources on the richness of methanol-utilizers in the bulk soil and rhizosphere is largely unknown. Therefore, the current study was planned to isolate, characterize and explore the richness of cultivable methylotrophs from the bulk soil and rhizosphere of a paddy field using media with varying nitrogen sources. Our data revealed that more genera of methylotrophs, including Methylobacterium, Ancylobacter, Achromobacter, Xanthobacter, Moraxella, and Klebsiella were enriched with the nitrate-based medium compared to only two genera, Hyphomicrobium and Methylobacterium, enriched with the ammonium-based medium. The richness of methylotrophic bacteria also differed substantially in the bulk soil as compared to the rhizosphere. Growth characterization revealed that majority of the newly isolated methanol-utilizing strains in this study exhibited better growth at 37 °C instead of 30 or 45 °C. Moreover, Hyphomicrobium sp. FSA2 was the only strain capable of utilizing methanol even at elevated temperature 45 °C, showing its adaptability to a wide range of temperatures. Differential carbon substrate utilization profiling revealed the facultative nature of all isolated methanol-utilizer strains with Xanthobacter sp. TS3, being an important methanol-utilizer capable of degrading toxic compounds such as acetone and ethylene glycol. Overall, our study suggests the role of nutrients and plant-microbial interaction in shaping the composition of methanol-utilizers in terrestrial environment.

Improved electrochemical properties of graphite electrodes incubated with iron powders in rice-paddy fields boost power outputs from microbial fuel cells.

Studies have shown that the supplementation of anode-surrounding soil with zero-valent iron (ZVI) boosts power outputs from rice paddy-field microbial fuel cells (RP-MFCs). In order to understand mechanisms by which ZVI boosts outputs from RP-MFCs, the present study operated RP-MFCs with and without ZVI, and compositions of anode-associated bacteria and electrochemical properties of graphite anodes were analyzed after 3-month operation. Metabarcoding using 16S rRNA gene fragments showed that bacterial compositions did not largely differ among these RP-MFCs. Cyclic voltammetry showed improved electrochemical properties of anodes recovered from ZVI-supplemented RP-MFCs, and this was attributed to the adhesion of iron-oxide films onto graphite surfaces. Bioelectrochemical devices equipped with graphite anodes recovered from ZVI-supplemented RP-MFCs generated higher currents than those with fresh graphite anodes. These results suggest that ZVI is oxidized to iron oxides in paddy-field soil and adheres onto graphite anodes, resulting in the boost of power outputs from RP-MFCs.

Occurrence and water-sediment exchange of systemic insecticides and their transformation products in an agriculture-dominated basin.

Neonicotinoids (NEOs) and fipronil (FIP) are ubiquitous in aquatic environment, yet the transformation and water-sediment exchange are largely unknown for these systemic insecticides and their transformation products (TPs). Herein, occurrence, field-based partitioning coefficients, and fugacity fractions (ff) of NEOs, FIP, and their TPs were analyzed in the drainage and receiving rivers near a rice paddy field. NEOs and FIPs were frequently detected in the sediments with concentrations of TPs being often higher than the parent compounds. Average ff values of NEOs (0.944-1.00) were larger than those of FIPs (0.399-0.716), indicating NEOs had a greater tendency to diffuse from sediment into water. Similar as well-studied hydrophobic compounds, hydrophobicity was the main factor impacting the water-sediment exchange of moderately hydrophobic FIPs. Alternatively, electrostatic interactions governed the fate of hydrophilic NEOs in water-sediment system. The log Kd values of NEOs were positively correlated with their N/C ratios (p < 0.05), possibly because the negatively charged sediments (zeta potential were from -19.1 ± 0.6 to -5.84 ± 0.57 mV) generated electrostatic attraction with amino functional group. Our study highlighted the ubiquitousness of TPs and distinct water-sediment interaction for moderately hydrophobic and hydrophilic insecticides in an agriculture-dominated watershed.

Determination of quintrione in rice, rice husk and rice straw and exploration of its dissipation from rice straw.

A rapid and sensitive method for the identification and quantification of quintrione residue in brown rice, rice husk, and rice straw matrices was developed and validated. Samples were extracted with acetonitrile, purified with octadecylsilane (C18) and graphitized carbon black (GCB) sorbents, and quantified using ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS). The developed method exhibited excellent linearity (R2 ≥ 0.9988), and the limit of quantitation was 2 µg/kg in all matrices. The method also had outstanding trueness and recoveries (90.5-111.1%) at four spiked levels (2, 20, 200, and 2000 µg/kg) with intraday and interday precisions of 0.7-6.5% and 5.2-11.8%, respectively, in the three matrices. The applicability of the method was tested by determining the dissipation rate of quintrione in rice straw under field conditions, and the measured data fit the Hockey stick kinetic model with R2 values of 0.9349-0.9983. The half-lives of quintrione in rice straw ranged from 2.7 to 16.5 days. The results indicate that the method is effective and reliable for the detection of quintrione residue in rice paddy fields, and the dissipation data provide guidance for the safe application of quintrione.

Nitrogen fertilizer application in the rice-growing season can stimulate methane emissions during the subsequent flooded fallow period.

Winter-flooded rice paddy field (FR), characterized by water conserved in the field during the fallow period, is a typical cropping system in southwest China, leading to considerable methane (CH4) emissions. The effect of nitrogen (N) fertilization on CH4 emissions during rice-growing seasons is well studied in FR, further studies covering N fertilizer applied in the rice-growing seasons affects CH4 emissions during the subsequent fallow period is needed. Therefore, a field experiment was conducted in an FR of Sichuan province, China, with conventional N fertilized (CN) and N unfertilized (NN) treatments. The cumulative CH4 emission from CN treatment during the rice-growing season and the subsequent fallow period was 389 ± 29.4 and 158 ± 31.2 kg C ha-1, which were increased by 29.5% and 395% in comparison with the NN treatment, indicting N applied during the rice growing-season significantly facilitated CH4 emission during the subsequent fallow period. During the rice-growing season, higher CH4 emission from CN treatment could be attributed to elevated soil dissolved organic carbon (DOC) content that might have provided sufficient substrates for CH4 production. During the fallow period, as compared to NN treatment, higher CH4 emissions from CN treatment could be explained by greater linear regression slopes between CH4 fluxes, soil temperature and DOC to dissolved inorganic N (DIN) (DOC/DIN) ratio. Moreover, the structural equation model (SEM) described that the soil temperature exhibited the most significant effects on CH4 emissions for both treatments during the rice-growing season and subsequent fallow period. These findings are a major step forward to showing that N fertilizer applied in the rice-growing season could also affect CH4 emission during the subsequent fallow period, accompanying other soil parameters controlling CH4 emission.

Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field.

Strain TER-1T was isolated from water sampled from a rice paddy field in Taiwan. Cells were Gram-negative, aerobic, motile, rod-shaped and formed pink-coloured colonies. Optimal growth occurred at 25-30 °C, pH 6-7 and in the presence of 0.5 % NaCl. Strain TER-1T could grow on C1 compounds such as methanol, formic acid, methylamine and dimethylamine as sole carbon source, and carry methanol dehydrogenase gene, which supports its methylotrophic metabolism. The results of phylogenetic analyses based on the 16S rRNA gene sequence, methanol dehydrogenase gene sequence and coding sequences of 92 protein clusters indicated that strain TER-1T formed a phylogenetic lineage in the genus Methylobacterium. Strain TER-1T was most closely related to Methylobacterium isbiliense AR24T with 96.8 % 16S rRNA gene sequence similarity. Strain TER-1T showed 77.1-82.8 % average nucleotide identity and 16.4-20.2 % digital DNA-DNA hybridization identity with the strains of other Methylobacterium species. The major fatty acid of strain TER-1T was C18 : 1ω7c. The predominant hydroxy fatty acid was C18 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and two uncharacterized lipids. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of strain TER-1T was 71.9 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TER-1T should be classified in a novel species of the genus Methylobacterium, for which the name Methylobacterium oryzihabitans sp. nov. is proposed. The type strain is TER-1T (=BCRC 81157T=LMG 30931T=KCTC 62864T).

Rice-paddy field acts as a buffer system to decrease the terrestrial characteristics of dissolved organic matter exported from a typical small agricultural watershed in the Three Gorges Reservoir Area, China.

Agricultural watersheds are a crucial contributor of terrestrial dissolved organic matter (DOM) for the adjacent aquatic environment. Recently, ecological engineering of the buffer zone such as a rice-paddy field was established to reduce the export of nutrients and contaminants from a small agricultural watershed. However, the potential of the rice-paddy field to reduce the terrestrial signature of DOM is unclear. Therefore, two small agricultural sub-catchments (i.e., sub-1 and sub-2) with different land uses and hill slope angles in the Three Gorges Reservoir (TGR) area of China were studied from 2014 to 2015. The results showed that the terrestrial DOM signals are indicated by optical indices (SUVA254, SR, fluorescence index) in the steeper and more forest covered, but rice-paddy field buffered sub-catchment (i.e., sub-2) decreased significantly, as compared to the reference sub-catchment (i.e., sub-1). Regardless of seasonal variations, the rice-paddy field retained a buffering role to reduce the terrestrial property of DOM and the highest capacity was observed during the rice-growth period. However, during storm events, the differences of DOM properties for two sub-catchments were not significant, because the buffer system was weakened. Finally, environmental implications of the role of such a buffer zone in the TGR areas are discussed. These results demonstrate that rice-paddy fields are successful in mitigating the terrestrial property of exported DOM, but the weaker performance during storm events still needs to be considered.

Influence of Land Use on the Structural Feature of Sedimentary Humic Acids in Rivers in Northwest Hokkaido, Japan.

Colloidal organic matter is an important factor in our understanding of the transport of trace metals by rivers to coastal areas and the characteristics of organic matter in the sediment, including the effect of humic substances on the transport of such metals. The structural features of humic acids (HAs) derived from surface sediments collected from the mouths of four rivers in northwest Hokkaido, Japan, were evaluated from the perspective of land use in their basins. The sediments in two rivers (referred to as NS and SK) were lacking in HAs, but the sediments of the others (referred to as SM and PO) contained relatively high levels of HAs. UV-vis spectroscopic characteristics suggested that the HAs in SM and PO contained components derived from humified materials. The PO and SM basins contain rice paddy fields, and TMAH-py-GC/MS analysis showed that the pyrograms of paddy soil HA had a similar character to those of PO-HA and SM-HA samples. Thus, the differences of the structural features can be attributed to the land use in river basins. The findings indicate that the properties of organic river sediments are heavily influenced by the type of land use in the river basins.

Water quality impacts of irrigation return flow on stream and groundwater in an intensive agricultural watershed.

Irrigation return flow can include contaminants derived from agricultural practices, and then deteriorate the quality of surface and subsurface water within the watershed. Thus, it is important to estimate the effect of irrigation return flow on water chemistry/quality. To do that water samples were collected between November 2004 and December 2005 from stream and groundwater in a small watershed that contains extensive rice paddy fields. The water isotopic compositions represented seasonal variation, particularly in downstream of main channel and the tributary. In April and May, water samples in the downstream and tributary could not be explained by three-component (soil water, groundwater and rainfall) hydrograph separation models (THSM). These results indicated that the stream water was affected by high evaporation and that another water body (e.g. quick return flow) impacted on THSM. Plot of Cl/NO3 and NO3/HCO3 showed that the water chemistry of all water samples was mainly regulated by soil water and groundwater. In addition, the water chemistry was related to water derived from rice paddy fields (WR) and manure. Manure impacted the water chemistry in tributary, one of the shallow groundwaters and the deep groundwaters, whereas that water in downstream was affected by WR. On a plot of δ15NNO3 and δ18ONO3 values, many samples were in a cluster indicative of manure and on a denitrification line. These imply that irrigation return flow characterized by denitrification processes was involved in determining the water chemistry. We suggest that chemical and multi-isotopes approach combined with the THSM is useful to elucidate the sources and processes controlling water chemistry in stream associated with rice paddy fields.

PCPF-M model for simulating the fate and transport of pesticides and their metabolites in rice paddy field.

BACKGROUND: The PCPF-1 model was improved for forecasting the fate and transport of metabolites in addition to parent compounds in rice paddies. In the new PCPF-M model, metabolites are generated from the dissipation of pesticide applied in rice paddies through hydrolysis, photolysis and biological degradations. The methodology to parameterize the model was illustrated using two scenarios for which uncertainty and sensitivity analyses were also conducted. RESULTS: In a batch degradation experiment, the hourly forecasted concentrations of fipronil and its metabolites in paddy water were very accurate. In a field-scale experiment, the hourly forecasted concentrations of fipronil in paddy water and paddy soil were accurate while the corresponding daily forecasted concentrations of metabolites were adequate. The major contributors to the variation of the forecasted metabolite concentrations in paddy water and paddy soil were the formation fractions of the metabolites. The influence of uncertainty included in input parameters on the forecasted metabolite concentration was high during the peak concentration of metabolite in paddy water. In contrast, in paddy soil, the metabolite concentrations forecasted several days after the initial pesticide application were sensitive to the uncertainty incorporated in the input parameters. CONCLUSION: The PCPF-M model simultaneously forecasts the concentrations of a parent pesticide and up to three metabolites. The model was validated using fipronil and two of its metabolites in paddy water and paddy soil. The model can be used in the early stage of the pesticide registration process and in risk assessment analysis for the evaluation of pesticide exposure. © 2017 Society of Chemical Industry.

Characterization of Nivalenol-Producing Fusarium culmorum Isolates Obtained from the Air at a Rice Paddy Field in Korea.

Together with the Fusarium graminearum species complex, F. culmorum is a major member of the causal agents of Fusarium head blight on cereals such as wheat, barley and corn. It causes significant yield and quality losses and results in the contamination of grain with mycotoxins that are harmful to humans and animals. In Korea, F. culmorum is listed as a quarantine fungal species since it has yet to be found in the country. In this paper, we report that two isolates (J1 and J2) of F. culmorum were collected from the air at a rice paddy field in Korea. Species identification was confirmed by phylogenetic analysis using multi-locus sequence data derived from five genes encoding translation elongation factor, histone H3, phosphate permease, a reductase, and an ammonia ligase and by morphological comparison with reference strains. Both diagnostic PCR and chemical analysis confirmed that these F. culmorum isolates had the capacity to produce nivalenol, the trichothecene mycotoxin, in rice substrate. In addition, both isolates were pathogenic on wheat heads and corn stalks. This is the first report on the occurrence of F. culmorum in Korea.