Cornfield Soil Research Articles

Bacterial community assembly and antibiotic resistance genes in soils exposed to antibiotics at environmentally relevant concentrations.

Understanding how bacterial community assembly and antibiotic resistance genes (ARGs) respond to antibiotic exposure is essential to deciphering the ecological risk of anthropogenic antibiotic pollution in soils. In this study, three loam soils with different land management (unmanured golf course, dairy-manured pasture, and swine-manured cornfield) were spiked with a mixture of 11 antibiotics at the initial concentration of 100 and 1000 μg kg-1 for each antibiotic and incubated over 132 days, mimicking a scenario of pulse disturbance and recovery in soils, with unspiked soil samples as the control treatment. The Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP) analysis demonstrated that drift and dispersal limitation contributed to 57%-65% and 16%-25%, and homogeneous selection 12%-16% of soil bacterial community assembly. Interestingly, antibiotic exposure to 1000 μg kg-1 level significantly increased the contribution of drift to community assembly, largely due to the positive response from Acidobacteria-6 in the golf course and pasture soilsand from Chthoniobacteraceae in the cornfield soil to the antibiotic exposure. However, ARG abundance and diversity in the three soils exhibited antibiotics-independent temporal fluctuations, but were associated with the changes in soil bacterial communities over time. This study provides the first insight into the relative contributions of different bacterial community assembly processes in soils upon antibiotic exposure at environmentally relevant concentrations.

Mapping of Cornfield Soil Salinity in Arid and Semi-Arid Regions

Mapping of Cornfield Soil Salinity in Arid and Semi-Arid Regions

Pesticide residues in corn and soil of corn fields of Khuzestan, Iran, and potential health risk assessment

Corn is the second most plentiful cereal grown for human consumption. Corn has several pests and diseases and various kind of pesticides are used for controlling these, and reducing their damage. In this study, 49 pesticide residues in 34 corn samples and nine corn field soil samples collected from eight cities of Khuzestan province as the main agricultural products in Iran were analyzed using a miniaturized QuEChERS extraction method. In addition, non-carcinogen and carcinogen health risk assessments were evaluated. Indoxacarb, metribuzin, propamocarb, and thiabendazole residues were detected in some corn samples. In addition, atrazine, cymoxanil, and propamocarb residues were found in some corn field soil samples. Results indicated that 35% of corn samples had at least one pesticide, of course, less than the maximum residue limit (MRL), except thiabendazole in 12 samples includes residue more than the acceptable limit. In addition, the Hazard index (HI) of corn samples was 1.83 × 10−4 and 8.53 × 10−4 in adults and children, respectively. No significant carcinogenic risk threatens corn consumers.

Impacts of Soil Moisture and Fertilizer on N2O Emissions from Cornfield Soil in a Karst Watershed, SW China

Incubation experiments using a typical cornfield soil in the Wujiang River watershed, SW China, were conducted to examine the impacts of soil moisture and fertilizer on N2O emissions and production mechanisms. According to the local fertilizer type, we added NH4NO3 (N) and glucose (C) during incubation to simulate fertilizer application in the cornfield soil. The results showed that an increase in soil moisture and fertilizer significantly stimulated N2O emissions in cornfield soil in the karst area, and it varied with soil moisture. The highest N2O emission fluxes were observed in the treatment with nitrogen and carbon addition at 70% water-filled pore space (WFPS), reaching 6.6 mg kg−1 h−1, which was 22,310, 124.9, and 1.4 times higher than those at 5%, 40%, and 110% WFPS, respectively. The variations of nitrogen species indicated that the production of extremely high N2O at 70% WFPS was dominated by nitrifier denitrification and denitrification, and N2O was the primary form of soil nitrogen loss when soil moisture was >70% WFPS. This study provides a database for estimating N2O emissions in cropland soil in the karst area, and further helped to promote proper soil nitrogen assessment and management of agricultural land of the karst watersheds.

Effects of thifluzamide on soil fungal microbial ecology

Thifluzamide, a succinate dehydrogenase inhibitor fungicide, has been used extensively for many diseases control and has the risk of accumulation in soil ecology. In order to study the ecotoxicity of thifluzamide to soil fungal communities, typical corn field soils in north (Tai’an) and south (Guoyang) China were treated with thifluzamide (0, 0.1, 1.0 and 10.0 mg/kg) and incubated for 60 days. Thifluzamide exposure promoted soil basal respiration, and significantly reduced the number of soil culturable fungi and the abundance of soil fungi (RT-qPCR) in middle and late treatment period (15, 30, 60 days). Illumina Mi-Seq sequencing revealed that thifluzamide could reduce fungal alpha diversity (Sobs, Shannon, Simpson indexes) and change fungal community structure. FUN Guild analysis showed that the relative abundance of Undefined Saprotroph increased after the thifluzamide treatment, whereas that of Plant Pathogen decreased, and we concluded that exposure to thifluzamide could change the function of soil fungi. This study evaluated the soil ecological risk caused by thifluzamide’s release into soil, providing a basis for its rational application.

Changes in Soil Organic Carbon and Its Labile Fractions after Land Conversion from Paddy Fields to Woodlands or Corn Fields

Land use change could significantly affect soil organic carbon (SOC) and other soil chemical properties. However, the responses of soil labile C fractions at different soil depths to land-use change are not still clear. The aim of this study was to investigate the effect of paddy field conversion on woodlands or corn fields on total soil organic C (TOC) and its labile C fractions including particulate organic C (POC), microbial biomass C (MBC), and potassium permanganate-oxidizable C (KMnO4–C) along a 0–100 cm soil profile. Our results indicate that soil TOC concentrations increased by 3.88 g kg−1 and 3.47 g kg−1 in the 0–5 cm soil layer and 5.33 g kg−1 and 4.68 g kg−1 in the 5–20 cm soil layer during 13 years after the conversion from paddy fields to woodlands and corn fields, respectively. In the 20–40 cm soil layer, the woodlands had the highest TOC concentration (12.3 g kg−1), which was 5.13 g kg−1 and 3.5 g kg−1 higher than that of the paddy and corn fields, respectively. The increase in TOC was probably due to the absence of soil disturbance and greater root residue input into the woodland soil. In corn fields, pig manure addition contributed to the increase in soil organic C concentrations. In addition, the proportion of soil KMnO4–C increased after conversion from paddy fields to woodlands or corn fields in the 0–40 cm soil layer, ranging from 39.9–56.6% for the woodlands and 24.6–32.9% for the corn fields. The soil POC content was significantly higher in woodland and corn field soils than in paddy field soils at lower soil depths (5–40 cm). However, there were no differences in MBC contents in the whole soil profile between the woodlands and paddy fields. The KMnO4–C and MBC was the most important factor affecting the CMI values through the whole 0–100 cm soil profile. Overall, converting paddy fields to woodlands or corn fields increased the TOC and labile C fractions in the 0–40 cm soil layer. Future studies should focus on the response of the deeper soil C pool to land-use change.

Effects of Corn Stalks and Urea on N2O Production from Corn Field Soil

Returning corn stalks to the field is an important and widely used soil management practice which is conducive to the sustainable development of agriculture. In this study, the effects of corn stalks and urea on N2O production in corn field soil were investigated through a 21-day incubation experiment. This study showed that increasing amounts of urea added to soil with a history of corn cultivation leads to increasing overall N2O emissions, by increasing both the intensity and the duration of emissions. Although N2O production was affected primarily by urea-derived NH4+-N and NO3−-N, its main source was native soil nitrogen, which accounted for 78.5 to 94.5% of N2O. Returning corn stalk residue to the field reduced the production of N2O, and the more urea was applied, the stronger the effect of corn residue on reducing N2O emissions. Combining the application of corn stalks and urea could reduce the concentration of NH4+-N and NO3−-N derived from urea, and then reduce the substrate required for N2O production in nitrification and denitrification processes. In addition, the combined application of corn stalks and urea could effectively inhibit the abundance of key N2O-producing genes AOA amoA, nirS and nirK.

Genome Sequence of Linnemannia hyalina Strain SCG-10, a Cold-Adapted and Nitrate-Reducing Fungus Isolated from Cornfield Soil in Minnesota, USA.

ABSTRACTWe report here the genome sequence of Linnemannia hyalina strain SCG-10, a cold-adapted and nitrate-reducing fungus isolated from soil. The genome of strain SCG-10 (51.6 Mbp) contained 12,693 protein-coding sequences.

The Response of Critical Microbial Taxa to Litter Micro-Nutrients and Macro-Chemistry Determined the Agricultural Soil Priming Intensity After Afforestation.

Afforestation with trees and shrubs around cropland can effectively decrease soil degradation and avoid sand storms, but subsequent modification of litter quality accelerates the degradation of native organic matter via the soil priming effect (PE). Although carbon accumulation in agricultural soils after afforestation was widely studied, little is known about the extent to which soil organic carbon (SOC) mineralization is induced by complex residue input in agro-forest-grass composite ecosystems. Here, we mixed corn field soil and litter of afforestation tree and shrub species together in a micro-environment to quantify the effects of litter-mixture input on farmland soil priming associated with afforestation. Additionally, we studied the responses of bacterial and fungal species to litter chemistry, with the aim to identify the litter and microbial driver of soil priming. The results showed that soil priming was accelerated by different litter addition which varied from 24 to 74% of SOC mineralization, suggesting that priming intensity was relatively flexible and highly affected by litter quality. We also find that the macro-chemistry (including litter carbon, nitrogen, lignin, and cellulose) directly affects priming intensity, while micro-chemistry (including litter soluble sugar, water-soluble phenol, methanol-soluble phenol, and condensed tannin) indirectly influences priming via alteration to dominant bacterial taxa. The stepwise regression analysis suggested that litter nitrogen and cellulose were the critical litter drivers to soil priming (r2 = 0.279), and the combination of bacterial phylum Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and fungal taxa Eurotiomycetes was a great model to explain the priming intensity (r2 = 0.407).

A mixed culture performing nitrite-dependent anaerobic methane oxidation and the nitrite removal mechanism revealed by high-throughput sequencing

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been regarded as a promising effective approach to nitrogen removal from wastewater. However, n-DAMO bacteria are very difficult to be enriched in biological wastewater treatment processes. An anaerobic sequencing batch reactor (AnSBR) was introduced in the present study for the enrichment of n-DAMO bacteria with cornfield soil as inoculum. Fed with nitrite (NO2−) and methane as the specific substrates, a NO2− load removal as high as 46.16 mg/(L·d) was obtained in the AnSBR since the 232nd day of enrichment culturing, though the relative abundance of Candidatus Methylomirabilis referring to n-DAMO bacteria was 2.37% in the acclimatized mixed culture. High-throughput sequencing of the obtained mixed culture revealed that the community structure was complex with the coexistence of n-DAMO bacteria, methanotrophs, heterotrophic denitrifying bacteria and hydrolytic fermentation bacteria. Analysis of interactions among the prevalent microbial populations suggested that Candidatus Methylomirabilis had played a key role in the metabolic network of the mixed culture. The research work presented a novel approach to the enrichment of n-DAMO bacteria from cornfield soil and was helpful in understanding the role of n-DAMO bacteria in complex matrices.

Draft Genome Sequences of 20 Aspergillus flavus Isolates from Corn Kernels and Cornfield Soils in Louisiana.

Aspergillus flavus is a common saprophyte and opportunistic fungal pathogen that infects plants, animals, and humans. It also produces numerous toxic and nontoxic secondary metabolites. Here, we report the draft genome sequences of 20 A. flavus isolates, belonging to 16 vegetative compatibility groups, from Louisiana corn kernels and cornfield soils.

Effects of Short-Term Application of Chemical and Organic Fertilizers on Bacterial Diversity of Cornfield Soil in a Karst Area

Among karst mountain agricultural fertilization measures, the partial replacement of chemical fertilizers with organic fertilizers is important for protecting its vulnerable mountain environment and developing ecologically-friendly agriculture. In this study, we investigated the effects of short-term organic fertilizer application on the bacterial diversity of maize soil in karst areas and the potential of using organic fertilizer as a partial substitute for chemical fertilizers. Two maize fields with different parent materials in a karst region were selected for a short-term field control experiment using chemical fertilizer and organic fertilizer treatment, combined with the high-throughput sequencing method of 16S rDNA gene amplicons. (i) The soil physicochemical properties and bacterial diversity of different parent material soil are different, but the main dominant bacterial types are similar. (ii) Short-term organic fertilizer treatment, rather than chemical fertilizer treatment, increased the bacterial richness significantly, especially for some functional bacteria (such as Nitrospira, Gemmatimonas). (iii) Analysis of the correlation between environmental factors and bacterial diversity indicated that soil pH and total P had the most significant effects on bacterial community structure (r = 0.91, p = 0.001; r = 0.33, p = 0.001). This study showed that it is an effective method to maintain a richer bacterial community and increasing the abundance of some functional bacteria by increasing organic fertilizers and reducing chemical fertilizers in the farm soil in karst regions, which could also be applied to other fragile agricultural ecosystems in the world.

Soil properties and heavy metal concentrations affect the composition and diversity of the diazotrophs communities associated with different land use types in a mining area

Biological nitrogen fixed by diazotrophs is important because it is the largest natural source of nitrogen to support primary productivity and maintain ecosystem sustainability when anthropogenic nitrogen inputs are lacking, especially in mining areas. The present study selected six different land use types (a corn field, a vegetable field, an area of shrubs, a mine tailing, a forest and a citrus orchard) as variables related to the mining activities around the Siding mining area, Liuzhou, Guangxi Province, China. A 0–10 cm soil layer was sampled, and the heavy metal concentrations and soil physicochemical properties were measured. Illumina MiSeq sequencing technology was used to analyze the abundance and structural diversity of the diazotroph community. The distribution of diazotroph assemblages among the different land use types and the main soil environmental properties that drive diazotroph community compositions were determined. The results indicated that the phylum Cyanobacteria (85.89%) was the most dominant taxon in the diazotrophic community in the citrus orchard. However, in the soils of the five other land use types, Proteobacteria was the most dominant taxon in the diazotrophic community, with a high abundance that ranged from 60.08% to 99.96%. Spearman's correlation analysis and redundancy analysis results indicated that the soil organic matter (OM) content in the citrus orchard was significantly higher than that in other areas, and the difference in soil OM content might be the main reason for the difference in the diazotrophic communities. The diazotrophic communities and their associated diversity under different land use types were driven by soil heavy metal and soil N (including NH4+-N, NO3−-N and total N (TN)) contents. Specifically, TN was highly correlated with the NMDS1 score of the soil diazotrophic community, which indicated that the soil TN content was the main reason for the high similarity among the diazotrophic communities in the corn field, vegetable field and shrub soils. Overall, our study offers a detailed description of the characteristics of the diazotroph community structure under different land use types around a mining area.

유기농 옥수수밭에서 경운이 토양 유기물 함량 및 미생물군집에 미치는 영향

유기농 옥수수밭에서 경운이 토양 유기물 함량 및 미생물군집에 미치는 영향

Pseudomonas bijieensis sp. nov., isolated from cornfield soil.

Strain L22-9T, a Gram-stain-negative and rod-shaped bacterium, motile by one polar flagellum, was isolated from cornfield soil in Bijie, Guizhou Province, PR China. Based on 16S rRNA gene sequences, it was identified as a Pseudomonas species. Multilocus sequence analysis of concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences showed that strain L22-9T formed a clearly separated branch, located in a cluster together with Pseudomonas brassicacearum LMG 21623T, Pseudomonas kilonensis DSM 13647T and Pseudomonas thivervalensis DSM 13194T. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) confirmed that strain L22-9T should be classified as a novel species. It was most closely related to P. kilonensis DSM 13647T with ANI and dDDH values of 91.87 and 46.3 %, respectively. Phenotypic features that can distinguish strain L22-9T from P. kilonensis DSM 13647T are the assimilation ability of N-acetyl-d-glucosamine, poor activity of arginine dihydrolase and failure to ferment ribose and d-fucose. The predominant cellular fatty acids of strain L22-9T are C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The respiratory quinones consist of Q-9 and Q-8. The polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipids, two unidentified aminophospholipids and an unidentified glycolipid. Based on the evidence, we conclude that strain L22-9T represents a novel species, for which the name Pseudomonas bijieensis sp. nov. is proposed. The type strain is L22-9T (=CGMCC 1.18528T=LMG 31948T), with a DNA G+C content of 60.85 mol%.

Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures

Land application of animal manure could change the profiles of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial communities in receiving soils. Using high-throughput real-time quantitative PCR and 16S rRNA amplicon sequencing techniques, this study investigated the ARGs and bacterial communities in field soils under various crop (corn and pasture) and manure (swine and dairy) managements, which were compared with those of two non-manured reference soils from adjacent golf course and grassland. In total 89 unique ARG subtypes were found in the soil samples and they conferred resistance via efflux pump, cellular protection and antibiotic deactivation. Compared to the ARGs in the golf course and grassland soils (28 and 34 subtypes respectively), manured soils generally had greater ARG diversity (36–55 subtypes). Cornfield soil frequently receiving raw swine manure had the greatest ARG abundance. The short-term (one week) application of composted and liquid swine manures increased the diversity and total abundance of ARGs in cornfield soils. Intriguingly the composted swine manure only marginally increased the total abundance of ARGs, but substantially increased the number of ARG subtypes in the cornfield soils. The network analysis revealed three major network modules in the co-occurrence patterns of ARG subtypes, and the hubs of these major modules (intl1-1, vanC, and pncA) may be candidates for selecting indicator genes for surveillance of ARGs in manured soils. The network analyses between ARGs and bacteria taxa revealed the potential host bacteria for the detected ARGs (e.g., aminoglycoside resistance gene aacC4 may be mainly carried by Acidobacteriaceae). Overall, this study highlighted the potentially varying impact of various manure management on antibiotic resistome and microbiome in cornfield and pasture soils.

Linking microbial community structure and product spectrum of rice straw fermentation with undefined mixed culture

Undefined mixed culture-based fermentation is an alternative strategy for biofuels and bioproducts production from lignocellulosic biomass without supplementary cellulolytic enzymes. Mixed culture produces mixed carboxylates. To estimate the relationship between microbial community structure and product spectrum, carboxylate production was initiated by mixed cultures with different microbial community structure. All the inoculum cultures were derived from the same enrichment culture from the combination of cattle manure, pig manure compost, corn field soil and rotten wood. Due to the differences in the preparation method and culture time, the inoculum cultures for batch fermentation had high similarity in microbial community structure, while the community structure of each inoculum culture for repeated batch fermentation differed from that of another. The inoculum cultures with similar community structure led to a similar product spectrum. In batch fermentation, the selectivity of main product butyric acid stabilized around 76%. The inoculum cultures with different community structures resulted in different product spectra. In repeated batch fermentation, the butyric acid content gradually decreased to 27%, and the by-product acetic acid content steadily increased to 56%. The other by-products including propionic, valeric and caproic acids were also increased. It is deduced that keeping the microbial community structure stable makes the basic and key precondition for steady production of specific carboxylic acid with undefined mixed culture.

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic

Investigation of microbial communities of soils contaminated by antimony (Sb) and arsenic (As) is necessary to obtain knowledge for their bioremediation. However, little is known about the depth profiles of microbial community composition and structure in Sb and As contaminated soils. Our previous studies have suggested that historical factors (i.e., soil and sediment) play important roles in governing microbial community structure and composition. Here, we selected two different types of soil (flooded paddy soil versus dry corn field soil) with co-contamination of Sb and As to study interactions between these metalloids, geochemical parameters and the soil microbiota as well as microbial metabolism in response to Sb and As contamination. Comprehensive geochemical analyses and 16S rRNA amplicon sequencing were used to shed light on the interactions of the microbial communities with their environments. A wide diversity of taxonomical groups was present in both soil cores, and many were significantly correlated with geochemical parameters. Canonical correspondence analysis (CCA) and co-occurrence networks further elucidated the impact of geochemical parameters (including Sb and As contamination fractions and sulfate, TOC, Eh, and pH) on vertical distribution of soil microbial communities. Metagenomes predicted from the 16S data using PICRUSt included arsenic metabolism genes such as arsenate reductase (ArsC), arsenite oxidase small subunit (AoxA and AoxB), and arsenite transporter (ArsA and ACR3). In addition, predicted abundances of arsenate reductase (ArsC) and arsenite oxidase (AoxA and AoxB) genes were significantly correlated with Sb contamination fractions, These results suggest potential As biogeochemical cycling in both soil cores and potentially dynamic Sb biogeochemical cycling as well.

Characterization and Distribution of Clay Minerals in Corn Field Soils in Korea

Distribution of clay minerals separated from clay fraction of corn fields in Korea has been investigated along with their characterization. Crystalline phases of the clay minerals were identified by powder X-ray diffraction (XRD) pattern, and their relative chemical compositions were analyzed by X-ray fluorescence spectrometry (XRF). The soils were found to have pH 6.4, organic matter 37.2 g kg-1, available P2O5 599 mg kg-1, respectively, and exchangeable K, Ca and Mg were 1.2, 7.3 and 1.8 cmolc kg-1, respectively. Major primary minerals consisted mainly of quartz and mica, and kaolinite and chlorite were identified as major secondary clay minerals. For most of soils, mica phase was identified to be muscovite rather than biotite. The average contents of SiO2, Al2O3 and Fe2O3 were 43.7, 23.6 and 8.8%, respectively, although they were different with the locations.Representative XRD patterns of clay fractions from corn fields.

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA.

In this study, we investigated the influence of heavy metals (HM) on total soil bacterial population and its diversity pattern from 10 km distance of a Zinc smelter in Feng County, Qinling Mountain, China. We characterized and identified the bacterial community in a HM polluted soil using 16S rDNA technology. Out results indicated that the maximum soil HM concentration and the minimum bacterial population were observed in S2 soil, whereas bacterial diversity raised with the sampling distance increased. The bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria in cornfield soils, except Fimicutes phylum which dominated in hilly area soil. The soil CEC, humic acid (HA)/fulvic acid (FA) and microbial OTUs increased with the sampling distance increased. Shewanella, Halomonas and Escherichia genera were highly tolerant to HM stress in both cultivated and non-cultivated soil. Finally, we found a consistent correlation of bacterial diversity with total HM and SOM along the sampling distance surrounding the zinc smelter, which could provide a new insight into the bacterial community-assisted and phytoremediation of HM contaminated soils.