Non-agricultural Soils Research Articles

Micobiota parasitária de escleródios de Sclerotinia sclerotiorum isolada de solos da fronteira oeste do Rio Grande do Sul

O objetivo do presente trabalho foi identificar a diversidade da micobiota parasitária e o tempo decorrido até o início do parasitismo de escleródios de Sclerotinia sclerotiorum em solos da fronteira oeste do Rio Grande do Sul (RS). Foram coletados solos agrícolas e não agrícolas de cinco localidades na fronteira oeste do Rio Grande do Sul. O isolamento dos fungos foi realizado por meio do teste de iscas, sendo que as iscas foram os escleródios do fitopatógeno, os quais permaneceram enterrados no solo durante 15, 30 e 60 dias. Os fungos foram identificados em nível de gênero. Os gêneros fúngicos encontrados parasitando escleródios foram: Trichoderma, Penicillium, Aspergillus, Fusarium, Pythium (Cromista), Clonostachys rosea (Gliocladium), Chaetomium, Curvularia, Phytophthora (Cromista), Rhizopus, Lichtheimia (Absidia), Mucor, Acremonium, Periconia e Isaria. Observou-se que os escleródios foram parasitados pelos fungos até 15 dias depois de serem enterrados, e deste período em diante apenas a frequência de ocorrência dos fungos mudou. Concluiu-se que os gêneros fúngicos Isaria, Periconia, Acremonium, Lichtheimia (Absidia), Phytophthora, Curvularia e Chaetomium são encontrados em solos agrícolas e não agrícolas na fronteira oeste do RS, e não foram citados anteriormente em outros trabalhos. Existe diversidade de fungos parasitários de escleródios de S. sclerotiorum nos solos da fronteira oeste do RS, os quais podem ser utilizados em experimentos para compor um programa de controle biológico desse fitopatógeno. Os escleródios são parasitados pelos fungos durante até 15 dias, após os mesmos serem enterrados no solo.

Concentration and Distribution of Fe, Al, Mn and Cr in Soils

The concentration and distribution of metal (Fe, Al, Mn and Cr) elements in agricultural and non-agricultural soils were investigated in upstream of the Pearl River, China. The result showed that total Fe, Al and Cr concentrations in agricultural soils were higher than those in non-agricultural soils, while total Mn concentrations in agricultural soils were lower than those in non-agricultural soils, indicating that agricultural input, such as water irrigation, fertilizer and pesticide application, may have led to the accumulation of Fe, Al and Cr in agricultural soils. Total concentrations of the metal elements in agricultural and non-agricultural soils were compared with the background values of Yunnan soil, the result showed Fe, Al, Mn and Cr were lower in both agricultural and non-agricultural soils in the study area.

Concentration and Distribution of Metal Elements in Soils near a Upstream of the Pearl River, China

The concentration and distribution of metal (Mg, K, Ca and Na) elements in agricultural and non-agricultural soils were investigated in upstream of the Pearl River, China. The result showed that total Mg, K, Ca and Na concentrations in agricultural soils were higher than those in non-agricultural soils, indicating that agricultural input, such as water irrigation, fertilizer and pesticide application, may have led to the accumulation of Mg, K, Ca and Na in agricultural soils. Total concentrations of the metal elements in agricultural and non-agricultural soils were compared with the background values of Yunnan soil, the result showed Mg, K and Na were lower in both agricultural and non-agricultural soils in the study area, while Ca was relatively higher, which were possibly due to Karsts geographic environment in the study area.

Chemical Speciation of Metal Elements in Agricultural and Non-Agricultural Soils

The chemical speciation of metal (Fe, Al, Mn and Cr) elements in agricultural and non-agricultural soils was investigated in upstream of the Pearl River, China. The result showed that Fe, Al and Cr in most of the samples, residual fractions accounted for more than 80% of their total concentrations. Mn in most of the samples, the reducible fractions were more than 40%, and generally more than residual fractions, oxidizable and weak acid soluble fractions. The mobility factors (MF) of Mn were the highest in both agricultural and non-agricultural soils, suggesting that the mobility of Mn were the strongest among the four metal elements. The MFs of Fe and Cr were almost zero, suggesting their mobility were low.

Chemical Speciation of Mg, K, Ca and Na in Soils

The chemical speciation of metal (Mg, K, Ca and Na) in agricultural and non-agricultural soils was investigated in upstream of the Pearl River, China. The result showed that the four metals speciation distributions of the agricultural soils were similar to those of the non-agricultural soils. Mg were dominated by the residual fraction, the order of Mg in each fraction was residual fraction > weak acid soluble fraction reducible fraction > oxidizable fraction. The distribution patterns of Na and K were similar, in most of the samples, the orders of Na and K in each fraction were residual fraction > weak acid soluble fraction > oxidizable fraction > reducible fraction. The order of Ca in each fraction was weak acid soluble fraction > reducible fraction > oxidizable fraction residual fraction. The bioavailability of Ca in the area was very high in both agricultural and non-agricultural soils.

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.

Assessment of soil geochemistry around some selected agricultural sites of Sri Lanka

Farming is the major source of income for the villagers of North-central Sri Lanka. However, chronic kidney disease of unknown etiology is a major health hazard in the area and it is assumed that agricultural contaminants are the major causative agents. This study focuses on the geochemistry of soils in the area to determine possible natural and anthropogenic impacts of the problem. X-ray fluorescence analysis was used to determine the abundance of selected major and trace elements. Results show that geo-enrichment for many elements indicates slight to significant variations between agricultural and non-agricultural soils. Geoaccumulation index (I geo) shows higher pollution levels of Pb and V (2 < I geo < 3) and very lower pollution levels of As, Zn, Cu, Fe and Mn (1 < I geo < 2) in agricultural soils. However, I geo for non-agricultural soils implies lack of contaminations (I geo < 1). Positive correlations of As with Pb and Zn and negative correlations with Cu, Ni and Cr suggest that they may have derived from different sources such as sulfide minerals of basement rocks, fertilizers and agrochemicals. The results of this study suggest that there is no significant threat from As and other trace elements to soils. The accumulation of these elements in agricultural fields may have been effectively controlled by seasonal farming practices. However, there is a potential environmental risk from elements such as Pb and V due to their significant enrichment in soils.

Determining Potential for Microbial Atrazine Degradation in Agricultural Drainage Ditches

Passage of agricultural runoff through vegetated drainage ditches has been shown to reduce the amount of pesticides, such as atrazine, exiting out of agricultural watersheds. Previous studies have found that microbial communities in soil from fields treated with atrazine display enhanced rates of atrazine degradation. However, no studies have examined the potential for atrazine degradation in ditches used to drain these lands. The purpose of the current study was to determine the potential of the drainage ditch soil microbial community for atrazine degradation. Soil samples were collected from fields and adjacent drainage ditches and from nonagricultural land with no previous exposure to atrazine. Polymerase chain reaction analysis indicated widespread presence of atrazine degradation genes in fields and ditches. Potential for degradation was determined by following the decrease of atrazine in spiked soil samples over a 28-d incubation period. Greater than 95% of atrazine was degraded in field and ditch soils, whereas only 68.5 ± 1.3% was degraded in the nonagricultural control. Comparison with autoclaved soil samples indicated the primary mechanism of atrazine degradation in agricultural soils was microbially mediated, whereas its breakdown in nonagricultural soil appeared to be the byproduct of abiotic processes. Therefore, microbial communities in drainage ditch sediments have the potential to play a role in atrazine removal from agricultural runoff by breaking down atrazine deposited in sediments and limiting the amount of this herbicide carried into downstream ecosystems.

Distribution and speciation of metals (Cu, Zn, Cd, and Pb) in agricultural and non-agricultural soils near a stream upriver from the Pearl River, China

The distribution and chemical speciation of typical metals (Cu, Zn, Cd and Pb) in agricultural and non-agricultural soils were investigated in the area of Nanpan River, upstream of the Pearl River. The investigated four metals showed higher concentrations in agricultural soils than in non-agricultural soils, and the site located in factory district contained metals much higher than the other sampling sites. These observations suggested that human activities, such as water irrigation, fertilizer and pesticide applications might have a major impact on the distribution of metals. Metal speciation analysis presented that Cu, Zn and Cd were dominated by the residual fraction, while Pb was dominated by the reducible fraction. Because of the low mobility of the metals in the investigated area, no remarkable difference could be observed between upstream and downstream separated by the factory site.

Genotypic Characterization of Azotobacteria Isolated from Argentinean Soils and Plant‐Growth‐Promoting Traits of Selected Strains with Prospects for Biofertilizer Production

The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA), gibberellin (GA3) and zeatin (Z) biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2–18.2 μg IAA mL−1, 0.3–0.7 μg GA3 mL−1, and 0.5–1.2 μg Z mL−1. Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

Meta-Analysis of Environmental Impacts on Nitrous Oxide Release in Response to N Amendment

Atmospheric nitrous oxide (N2O) accounts for approximately 5% of the global greenhouse effect and destroys stratospheric ozone. Soils are the most important source of N2O, which is produced during nitrification and denitrification. To assess the impact of environmental variables and ecosystems on N2O flux, we performed a meta-analysis comparing N2O flux in N amended and matched control plots in non-agricultural soils. We found that N2O release increased with N amendment in the short term. Although there were few studies in shrubland, this ecosystem showed the greatest response. The N2O response to N amendment was greater in year-round studies and in studies with more measurements, but lower in longer studies. The N2O response was greater at higher latitudes and precipitation rates. We also observed an unexpected 55% decline in the N2O response to N amendment over the 23 years covered by the studies. This pattern may reflect a suppression of the N2O response from long-term N deposition accumulation, particularly in temperate regions. Although short term increases in reactive N entering natural systems may cause positive feedbacks to the release of N2O, this effect may diminish over time in locations with high rates of N deposition.

Long-term land use effects on soil microbial community structure and function

Microbial community diversity and structure, which underpin soil function, can in turn be impacted by land-use practices. In this study an agricultural site with consistent long term (+20 years) treatments and a non-agricultural site (grassland) were investigated to determine land-use effects on soil microbial community structure and function. We used a variety of methods to investigate microbial community structure, biomass, potential and actual function and soil physicochemical properties. All soils showed similar levels of bacterial diversity although community structure (bacterial, archaeal, fungal) differed under all treatments. Overall, our results indicate that despite evident differences in microbial community structure among all soils examined, there was little functional difference among soils under cultivation in the various cropping treatments. There were, however, clear differences in both function and structure between the agricultural and non-agricultural soils. All soils were very water limited, which was reflected in negligible actual rates of nitrification, denitrification and nitrogen fixation. Non-agricultural soils showed higher rates of potential nitrification, lower rates of potential denitrification, higher levels of C and N and higher microbial biomass. These findings have implications for understanding how land-use practices affect soil microbial community structure and function and ecosystem service provision.

Assessment of the impact of various mitigation options on nitrous oxide emissions caused by the agricultural sector in Europe

A European Union (EU-27) wide N2O emission estimate for the agricultural sector is presented, using the INTEGRATOR model, combined with detailed GIS-based environmental data and farming data. INTEGRATOR links various modules, calculating NH3, NOx, N2O, CO2, and CH4 emissions from housing and manure storage systems, agricultural and non-agricultural soils and surface waters, while accounting for the interaction between agricultural and non-agricultural systems through an emission-deposition model for NH3 and NOx. This study is limited to N2O emissions from housing and manure storage systems and agricultural soils. All emissions are based on N2O emission factors which depend on environment (weather and soil conditions), land use (grassland, arable land, crop residues), and management (type of manure and fertilizer, etc). We assessed the plausibility by a comparison of calculated present nitrous oxide emissions at country level with those derived by more simple emission factor approaches and detailed ecosystem models. The model was used to assess the impact of various farming practice packages to mitigate N2O emissions. For the agricultural sector of the EU-27, a total N2O emission of 347 kton N2O‒N is calculated for the year 2000, which is comparable to other estimates. The overall achievable reduction in N2O emissions with the evaluated mitigation measures is about 25%. For the EU-27, the most effective measures are balanced fertilization and maximum manure application, but this is highly variable per country.

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents.

A geochemical survey of trace elements in agricultural and non-agricultural topsoil in Dexing area, China

In China, soil pollution is very serious, which has jeopardized the ecology, food safety, the people's health, and even the sustainable development of agriculture. In order to investigate the soil pollution situation, a total of 874 agricultural and non-agricultural topsoil samples were collected from Dexing area, northeast of Jiangxi Province, China. The total elemental concentrations of 17 elements (As, Hg, Mo, Cd, Cr, Zn, Cu, Mn, Ti, Pb, Fe, Ca, K, Si, Al, Mg, and Na) were determined. The geochemical background and threshold was predicted with the method of the median ± median absolute deviation (MAD). The agricultural soil median concentration of trace elements was similar to that of the non-agricultural soil. In contrast to Jiangxi soil background of trace elements, the geochemical background of the study area was obviously higher. The maps of the pollution indices for As, Cd, Cr, Cu, Hg, Mn, Mo, Pb, Ti and Zn of non-agricultural soil and agricultural soils in the study area, showed that the highest level of pollution is distributed near and along the Lean River, especially in the neighboring and surrounding Dexing and Leping mining area.

Comparison of Streptomyces diversity between agricultural and non-agricultural soils by using various culture media.

Streptomycetes play a key role in the sustainability of agriculture and indicates the level of health of soil, especially when considering the richness of them that are involved in biological control of soil borne diseases. 20 different soil samples were taken from agricultural (7) and non-agricultural places (13) and populations of streptomycetes were quantified in order to select the general culture media that had better reflect the changes of these bacteria. The most efficient medium for the isolation of Streptomyces was starch casein agar by the addition of nystatin. Pretreatment of soil samples with CaCO3 (1%) increased the streptomycetes occurring on the isolation plates. To establish a correlation with soil physico-chemical parameters, such as pH, salt, N, P, K, Na, Fe, Zn and Cu were also determined, most of the correlations being significantly positive on the quantification of Streptomyces diversity. Streptomycete counts ranged from a high of 6.7 x 10 6 to a low of 2.3 x 10 6 cfu/g dry soil of non-agricultural soils. Streptomycetes constituted 4.8 to 45.8% of the total culturable bacterial community. Higher streptomycete densities were greatest in non-agricultural soils with an average of 14.0% compared to agricultural soils with average of 10.1%. These results suggest that these bacteria may be represent an unexplored resource for pharmaceutical drug discovery but also may provide additional disease control in agriculture.

A new concept for reduction of diffuse contamination by simultaneous application of pesticide and pesticide-degrading microorganisms

Pesticide residues and their transformation products are frequently found in groundwater and surface waters. This study examined whether adding pesticide-degrading microorganisms simultaneously with the pesticide at application could significantly reduce diffuse contamination from pesticide use. Degradation of the phenoxyacetic acid herbicides MCPA (4-chloro-2-methylphenoxyacetic acid) and 2,4-D (2,4-dichlorophenoxyacetic acid) was studied in soil microcosm experiments after simultaneous spraying of herbicide and herbicide-degrading bacteria on an agricultural soil and on a sand with low degradation potential. The latter represented pesticide use on non-agricultural soils poor in microbial activity. Degradation and possible loss of herbicidal effect were also tested in a system with plants and the amounts of bacteria needed to give satisfactory MCPA-degradation rate and the survival of degrading bacteria in formulated MCPA were determined. The results showed >80-99% degradation of 2,4-D and MCPA in soil within 1 day and >99% within 3 days after inoculation with 10(5)-10(7) herbicide-degrading bacteria g(-1) dry weight of soil. Enhanced degradation of MCPA was also obtained in the presence of winter wheat and white mustard without loss of the intended herbicidal effect on white mustard. The survival of an isolated MCPA-degrading Sphingomonas sp. in three realistic concentrations of formulated MCPA was very poor, showing that in practical applications direct contact between the microorganisms and the pesticide formulation must be precluded. The applicability and economic feasibility of the method and the information needed to obtain a useable product for field use are discussed.

The Effects of Anisotropy on In Situ Air Permeability Measurements

Previous research has established a correlation between air permeability (ka) and saturated hydraulic conductivity for agricultural soils based on ex situ air permeability (kex situ). In situ air permeability (kin situ) measurements in nonagricultural soils, however, have shown a decrease in correlation that may be attributed to soil anisotropy. Our objectives were: (i) to examine the effects of anisotropy on kin situ using a three‐dimensional air flow model; (ii) to develop a method to identify anisotropy using kin situ and kex situ measurements; and (iii) to determine the sample volume of an air permeameter as a function of the permeameter design and the anisotropy ratio. Numerical results showed that the ka measured in situ in anisotropic media results in some average of the horizontal and vertical permeabilities. The averaging depends on the degree of anisotropy and the ratio of the diameter to the insertion depth of the permeameter. Therefore, a shape factor developed for an isotropic soil can give unreliable results. We determined that paired in situ and ex situ permeability measurements can be used to infer the anisotropy ratio. This approach is more accurate if the vertical permeability, kaz, is higher than the horizontal, kax The sample volume does not extend outside of the air permeameter for high kax/kaz It is stretched vertically for low kax/kaz A field experiment showed qualitative agreement with model predictions, but anisotropy alone was not able to fully explain the difference between kin situ and kex situ

Asexual Reproduction of Phytophthora capsici as Affected by Extracts from Agricultural and Nonagricultural Soils

ABSTRACT Formation of sporangia and zoospores in species of Phytophthora is known to be influenced by soil microbial and chemical composition. In Phytophthora capsici, the study of the relationship of soil chemical composition to production of sporangia and zoospores has been limited. P. capsici is a soilborne pathogen of a wide array of vegetable crops, including chile pepper (Capsicum annuum) in New Mexico. Production of sporangia and zoospores by P. capsici was evaluated in extracts of soils from three different environments in New Mexico: (i) agricultural environments with a long history of chile pepper cropping and occurrence of P. capsici (CP), (ii) agricultural environments with no history of chile pepper cropping and no occurrence of P. capsici (Non-CP), and (iii) nonagricultural environments consisting of forests and rangelands (Non-Ag). There was a significant difference in production of P. capsici asexual propagules, expressed as natural log (number of sporangia x number of zoospores), among the three environments (P = 0.0298). Production of propagules was 9 to 13% greater in Non-Ag than in CP or Non-CP environments. Stepwise multiple discriminant analysis and canonical discriminant analysis identified the edaphic variables Na, pH, P, organic matter content, and asexual propagule production as contributing the most to the separation of the three environments. Two significant (P < 0.0001) canonical discriminant functions were derived with the first function, accounting for approximately 75% of the explained variance. Based on the two discriminant functions, approximately 93, 86, and 89% of observations in CP, Non-CP, and Non-Ag environments, respectively, were classified correctly. Soils from agricultural and nonagricultural environments differentially influence production of sporangia and zoospores in P. capsici, and soil samples could be effectively classified into agricultural and nonagricultural environments based on soil chemical properties and the production of asexual propagules by P. capsici in soil extracts.

The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria

The use of antibiotics at subtherapeutic concentrations for agricultural applications is believed to be an important factor in the proliferation of antibiotic-resistant bacteria. The goal of this study was to determine if the application of manure onto agricultural land would result in the proliferation of antibiotic resistance among soil bacteria. Chlortetracycline-resistant bacteria were enumerated and characterized from soils exposed to the manure of animals fed subtherapeutic concentrations of antibiotics and compared to the chlortetracycline-resistant bacteria from soils at farms with restricted antibiotic use (dairy farms) and from non-agricultural soils. No significant differences were observed at nine different study sites with respect to the numbers and types of cultivated chlortetracycline-resistant bacteria. Genes encoding for tetracycline resistance were rarely detected in the resistant bacteria from these sites. In contrast, soils collected from a tenth farm, which allowed manure to indiscriminately accumulate outside the animal pen, had significantly higher chlortetracycline-resistance levels. These resistant bacteria frequently harbored one of 14 different genes encoding for tetracycline resistance, many of which (especially tet(A) and tet(L)) were detected in numerous different bacterial species. Subsequent bacterial enumerations at this site, following the cessation of farming activity, suggested that this farm remained a hotspot for antibiotic resistance. In conclusion, we speculate that excessive application of animal manure leads to the spread of resistance to soil bacteria (potentially by lateral gene transfer), which then serve as persistent reservoir of antibiotic resistance.