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Field Soil (field + soil)
Kinds of Field Soil Selected AbstractsA methane-driven microbial food web in a wetland rice soilENVIRONMENTAL MICROBIOLOGY, Issue 12 2007Jun Murase Summary Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and 13C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria -related sequences were obtained from the ,heavy' rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the ,heavy' rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability. [source] Dissipation kinetics and mobility of chlortetracycline, tylosin, and monensin in an agricultural soil in Northumberland County, Ontario, CanadaENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2006Jules C. Carlson Abstract A robust high-throughput method was refined to extract three growth-promoting antibiotics, tylosin (TYL), chlortetracycline (CTC), and monensin (MON), from soil. Analysis was performed by electrospray liquid chromatography tandem mass spectrometry. Soil dissipation rate studies were performed in a farm field soil for antibiotics applied with and without manure. Tylosin, CTC, and MON followed first-order dissipation kinetics with half-lives of 4.5, 24, and 3.3 d, respectively, with the addition of manure and 6.1, 21, and 3.8 d, respectively, without manure. Manure application significantly increased TYL dissipation rate, perhaps because of the introduced microbial flora, but had no significant effect on CTC or MON. Monensin dissipation half-life was found to be much shorter in the field study than in a controlled laboratory study, perhaps because of differences in microbial communities. The antimicrobials were not highly mobile. Chlortetracycline was the only antibiotic detected at 25 to 35 cm depth and only up to 2% of the initial concentration in a sandy loam soil. These antibiotics are therefore expected to degrade primarily in agricultural soils before moving to greater depths or to groundwater in significant concentrations in most agricultural systems. [source] Effect of temperature change on the composition of the bacterial and archaeal community potentially involved in the turnover of acetate and propionate in methanogenic rice field soilFEMS MICROBIOLOGY ECOLOGY, Issue 2 2010Matthias Noll Abstract The microbial community structure was investigated together with the path of methane production in Italian rice field soil incubated at moderate (35 °C) and high (45 °C) temperature using terminal restriction fragment length polymorphism and stable isotope fractionation. The structure of both the archaeal and bacterial communities differed at 35 °C compared with 45 °C, and acetoclastic and hydrogenotrophic methanogenesis dominated, respectively. Changing the incubation of the 45 °C soil to different temperatures (25, 30, 35, 40, 45, 50 °C) resulted in a dynamic change of both microbial community structure and stable isotope fractionation. In all treatments, acetate first accumulated and then decreased. Propionate was also transiently produced and consumed. It is noteworthy that acetate was also consumed at thermophilic conditions, although archaeal community composition and stable isotope fractionation indicated that acetoclastic methanogenesis did not operate. Instead, acetate must have been consumed by syntrophic acetate oxidizers. The transient accumulation and subsequent consumption of acetate at thermophilic conditions was specifically paralleled by terminal restriction fragments characteristic for clostridial cluster I, whereas those of clostridial clusters I and III, Acidaminococcaceae and Heliobacteraceae, paralleled the thermophilic turnover of both acetate and propionate. [source] Bacterial quorum sensing and nitrogen cycling in rhizosphere soilFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Kristen M. DeAngelis Abstract Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N) mineralization. Most soil organic nitrogen is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate limiting for plant nitrogen accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease-specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared with bulk soil. Low-molecular-weight (MW) DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density-dependent group behavior. Because proteobacteria are considered major rhizosphere colonizers, we assayed the proteobacterial QS signals N -acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and nitrogen cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in seven of eight isolates disrupted enzyme activity. Many Alphaproteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of nitrogen-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere nitrogen mineralization. [source] The development and endophytic nature of the fungus Heteroconium chaetospiraFEMS MICROBIOLOGY LETTERS, Issue 2 2005Teruyoshi Hashiba Abstract The root endophytic fungus Heteroconium chaetospira was isolated from roots of Chinese cabbage grown in field soil in Japan. This fungus penetrates through the outer epidermal cells of its host, passes into the inner cortex, and grows throughout the cortical cells, including those of the root tip region, without causing apparent pathogenic symptoms. There are no ultrastructural signs of host resistance responses. H. chaetospira has been recovered from 19 plant species in which there was no disruption of host growth. H. chaetospira has a symbiotic association with Chinese cabbage. The fungus provides nitrogen in exchange for carbon. These associations are beneficial for the inoculated plants, as demonstrated by increased growth rate. When used as a preinoculum, H. chaetospira suppresses the incidence of clubroot and Verticillium yellows when the test plant is post-inoculated with the causal agents of these diseases. H. chaetospira is an effective biocontrol agent against clubroot in Chinese cabbage at a low to moderate soil moisture range and a pathogen resting spore density of 105 resting spores per gram of soil in situ. Disease caused by Pseudomonas syringae pv. macricola and Alternaria brassicae on leaves can be suppressed by treatment with H. chaetospira. The fungus persists in the roots and induces systemic resistance to the foliar disease. [source] Tracing solute infiltration using a combined method of dye tracer test and electrical resistivity tomography in an undisturbed forest soil profileHYDROLOGICAL PROCESSES, Issue 21 2010Jae Gon Kim Abstract An accurate prediction of solute infiltration in a soil profile is important in the area of environmental science, groundwater and civil engineering. We examined the infiltration pattern and monitored the infiltration process using a combined method of dye tracer test and electrical resistivity tomography (ERT) in an undisturbed field soil (1 m × 1 m). A homogeneous matrix flow was observed in the surface soil (A horizon), but a preferential flow along macropores and residual rock structure was the dominant infiltration pattern in the subsurface soil. Saturated interflow along the slopping boundaries of A and C1 horizons and of an upper sandy layer and a lower thin clay layer in the C horizon was also observed. The result of ERT showed that matrix flow started first in A horizon and then the infiltration was followed by the preferential flows along the sloping interfaces and macropores. The ERT did not show as much detail as the dye-stained image for the preferential flow. However, the area with the higher staining density where preferential flow was dominant showed a relatively lower electrical resistivity. The result of this study indicates that ERT can be applied for the monitoring of solute transportation in the vadose zone. Copyright © 2010 John Wiley & Sons, Ltd. [source] An improved method to extract RNA from soil with efficient removal of humic acidsJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2009Y. Wang Abstract Aims:, To remove humic substances from RNA extracted from soil for the study of bacterial gene expression in soil. Methods and Results:, A soil RNA extraction method was improved by optimization of lysis conditions and further purification by a spin column, to efficiently remove humic substances that may hinder enzymatic reactions of extracted RNA. Fluorescence spectrophotometry demonstrated that the improved method removed both humic and fulvic acids efficiently. Using the improved method, the signal of gene expression detected by real-time reverse transcription,polymerase chain reaction (RT-PCR) increased 10-fold compared with that using the previous method. Using the method, we extracted RNA from a sterilized field soil, which was inoculated with Pseudomonas putida KT2440 transformed with a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoate (3CB). Real-time RT-PCR performed using the extracted RNA as a template confirmed the induction of chloroaromatic degrading genes in 3CB-amended soil. Conclusions:, The modified soil RNA extraction method succeeded in removing the co-extracted humic substances from soil RNA efficiently and improving the detection efficiency of the bacterial gene expression in soil. Significance and Impact of the Study:, This improved method is a useful tool for the extraction of RNA to detect gene expression in soil. [source] To what extent are soil amendments useful to control Verticillium wilt?PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2009Nieves Goicoechea Abstract The genus Verticillium includes several species that attack economically important crops throughout the world. The control of Verticillium spp. becomes especially difficult when they form microsclerotia that can survive in the field soil for several years. It has been common practice to fumigate soil with chemicals such as methyl bromide and/or chloropicrin to control soil-borne fungal pathogens. Other chemicals that are used against Verticillium spp. are the antifungal antibiotic aureofungin, the fungicides benomyl, captan, carbendazim, thiram, azoxystrobin and trifloxystrobin and the plant defence activator acibenzolar- S -methyl. However, the potential risks involved in applying phytochemicals to crop plants for both the environment and human health, together with their limited efficacy for controlling Verticillium -induced diseases, support the need to find alternatives to replace their use or improve their efficacy. Soil amendment with animal or plant organic debris is a cultural practice that has long been used to control Verticillium spp. However, today the organic farming industry is becoming a significant player in the global agricultural production scene. In this review, some of the main results concerning the efficacy of several soil amendments as plant protectors against Verticillium spp. are covered, and the limitations and future perspectives of such products are discussed in terms of the control of plant diseases. Copyright © 2009 Society of Chemical Industry [source] PCR-based identification of Pythium spp. causing cavity spot in carrots and sensitive detection in soil samplesPLANT PATHOLOGY, Issue 5 2008S. S. Klemsdal On the basis of ITS sequences PCR primers were designed for the identification of the five Pythium species found to be most important for the development of carrot cavity spot in Norway: P. intermedium, P. sulcatum, P. sylvaticum, P. violae and P. ,vipa'. The P. ,vipa' isolates had a unique ITS sequence, differed morphologically from all other Pythium isolates, and thus probably represent a new species. The PCR primers were species-specific with no cross-reaction to other Pythium species or to fungal isolates from carrot tested. The detection limits varied for the different primer pairs. The two most sensitive assays allowed detection of as little as 5 fg DNA. All five Pythium species could be detected in lesions from diseased carrots. Weak positive signals were obtained from some carrot samples without symptoms. PCR assays allowed detection of pathogens in soil. In samples of soil known to produce cavity spots on cropped carrots, strong signals were obtained. In several soil samples more than one of the five Pythium species could be detected. The utilization of this diagnostic PCR assay in analysis of field soil and carrot tissue might in the future be exploited to reduce the incidence of this serious carrot disease. [source] Novel in vivo use of a polyvalent Streptomyces phage to disinfest Streptomyces scabies -infected seed potatoesPLANT PATHOLOGY, Issue 6 2001F. McKenna A highly virulent and polyvalent Streptomyces phage was isolated from a potato field near Albany, Western Australia. The efficacy of the isolated phage to disinfest seed potato tubers artificially inoculated with a common scab-causing streptomycete was evaluated. The phage suspension was prepared in a mini-bioreactor. Diseased potatoes were bathed in a phage suspension (1 × 109 plaque-forming units per mL) for 24 h. The suspension was constantly circulated within a novel 25 L phage bath by means of an air-sparging pipe driven from an air compressor. Phage-treated scab-affected seed potatoes planted into free-draining polystyrene boxes containing steam-pasteurized field soil produced tuber progeny with significantly (P < 0·05) reduced levels of surface lesions of scab (1·2%) compared with tubers harvested from nonphage-treated tubers (23%). The number of scab lesions was also significantly reduced (P < 0·05) by phage treatment of mother tubers. No significant differences were recorded in weight, size or number of harvested tubers from phage-treated or nontreated mother tubers. This is the first in vivo study that has used Streptomyces phage to significantly disinfest seed potatoes of Streptomyces scabies and thereby reduce contamination of soil from seed-tuber-borne inoculum and reduce infection of daughter tubers. [source] Development of a simulated earthworm gut for determining bioaccessible arsenic, copper, and zinc from soil,ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 7 2009Wai K. Ma Abstract Soil physicochemical characteristics and contamination levels alter the bioavailability of metals to terrestrialinvertebrates. Current laboratory-derived benchmark concentrations used to estimate risk do not take into account site-specific conditions, such as contaminant sequestration, and site-specific risk assessment requires a battery of time-consuming and costly toxicity tests. The development of an in vitro simulator for earthworm bioaccessibility would significantly shorten analytical time and enable site managers to focus on areas of greatest concern. The simulated earthworm gut (SEG) was developed to measure the bioaccessibility of metals in soil to earthworms by mimicking the gastrointestinal fluid composition of earthworms. Three formulations of the SEG (enzymes, microbial culture, enzymes and microbial culture) were developed and used to digest field soils from a former industrial site with varying physicochemical characteristics and contamination levels. Formulations containing enzymes released between two to 10 times more arsenic, copper, and zinc from contaminated soils compared with control and 0.01 M CaCl2 extractions. Metal concentrations in extracts from SEG formulation with microbial culture alone were not different from values for chemical extractions. The mechanism for greater bioaccessible metal concentrations from enzyme-treated soils is uncertain, but it is postulated that enzymatic digestion of soil organic matter might release sequestered metal. The relevance of these SEG results will need validation through further comparison and correlation with bioaccumulation tests, alternative chemical extraction tests, and a battery of chronic toxicity tests with invertebrates and plants. [source] Epifluorescence microscopy and image analysis of high-level polycyclic aromatic hydrocarbon contamination in soilsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2006J. Chadwick Roper Abstract Interactions between polycyclic aromatic hydrocarbons (PAHs) and soil are an important determinant of their chemical availability and transport. Laboratory examination of microscale PAH,soil interaction is limited by the availability of methods for particle-scale observation. Inverted epifluorescence microscopy, combined with digital photography and computer image analysis, was evaluated for specificity and linearity using dissolved PAHs. A pyrene filter (excitation wavelength, 360,400 nm; emission wavelength, 450,520 nm) gave nonspecific PAH fluorescence, and bias for fluoranthene, benzo[b]fluoranthene, benzo[g, h, i]perylene, and benz[a]anthracene was quantified in comparison to that for pyrene. Concentrations ranging from 1 to 10 mM for anthracene, fluoranthene, and pyrene and from 1 to 50 mM for naphthalene produced a linear response with low interpixel variability. Liquid-phase analyses validated use of the technique for the descriptive analysis of PAH distribution in solid samples, but liquid-phase calibration was not quantitative for spiked or field-contaminated soils. The mean luminance for three field soils was proportional to the values predicted from their chemically measured concentrations and to values from spiked, aged, uncontaminated materials. Image analysis of laboratory- and field-contaminated samples determined the area distribution of fluorescent intensity and the size of fluorescent areas exceeding a threshold luminance. These qualitative descriptions of the microscale spatial distribution of PAH contamination are presented as potential endpoints for future research on biogeochemical interactions in heavily contaminated solids. [source] Simulation of water flow and solute transport in free-drainage lysimeters and field soils with heterogeneous structuresEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2004H. M. Abdou Summary Lysimeters are valuable for studying the fate and transport of chemicals in soil. Large-scale field lysimeters are used to assess pesticide behaviour and radionuclide transport, and are assumed to represent natural field conditions better than laboratory columns. Field lysimeters are usually characterized by a free-draining lower boundary. As a result, the hydraulic gradient is disrupted, and leachate cannot be collected until the bottom of the lysimeter becomes saturated. We compared heterogeneously structured, free-drainage lysimeters and field soils with respect to water flow and solute transport. Numerical simulations were carried out in a two-dimensional heterogeneous sandy soil under unsaturated water flow conditions with the CHAIN_2D code. Three different soil structures (isotropic, horizontal, and vertical) were generated, and Miller,Miller similitude was used to scale the hydraulic properties of the soil. The results showed that ponding occurs at the bottom of the lysimeter for the three soil structures and that it occurred faster and was more pronounced with the vertical structure (preferential flow effect). Breakthrough curves of a conservative solute (bromide) showed that solutes are moving faster in the field than in the lysimeters. Fewer differences between lysimeters and field soils were found with the horizontal soil structure than with the isotropic and vertical structures. [source] Evaluation of PetrifilmÔ EC method for enumeration of E. coli from soilLETTERS IN APPLIED MICROBIOLOGY, Issue 5 2010A.D. Samarajeewa Abstract Aims:, To evaluate the suitability of commercially available PetrifilmÔ EC plates for enumeration of Escherichia coli from soil. Methods and Results:, A confirmed E. coli strain isolated from liquid swine manure was inoculated into sterilized sandy clay loam and loam soils at the concentrations of 102, 103, 105 CFU g,1 of soil. The efficiency of recovery on PetrifilmÔ EC plates for soils spiked with E. coli was compared with standard membrane filtration techniques on m-FC basal medium supplemented with 3-bromo-4-chloro-5-indoyl-,- d -glucopyranoside (BCIG) and most probable numbers (MPN) techniques in E. coli medium with 4-methylumbelliferyl-,- d -glucuronide (EC-MUG) broth. PetrifilmÔ EC and m-FC (BCIG) methods were then assessed for the ability to recover E. coli from field soils applied with swine manure. No significant differences (P > 0·05) were observed between PetrifilmÔ EC, m-FC (BCIG) and MPN methods for the recovery of E. coli from spiked samples, irrespective of soil type. However, recovery of E. coli from manure-applied field soil samples showed a significant difference (P < 0·05) between the PetrifilmÔ EC method and the m-FC method in enumerating E. coli possibly as a result of false positives on m-FC. Conclusion:, The PetrifilmÔ EC method is suitable for the enumeration of E. coli from soil with a detection limit of 10 CFU g,1 soil. Significance and Impact of the Study:, The commercially available PetrifilmÔ EC method is comparatively low cost, easy to use method for the enumeration of E. coli from soil without the need for further confirmation tests. [source] Sensitive detection of Ralstonia solanacearum in soil: a comparison of different detection techniquesPLANT PATHOLOGY, Issue 4 2000P. M. Pradhanang The sensitivity and specificity of various methods were compared for routine detection of Ralstonia solanacearum in a sandy loam soil. Populations fewer than 102 CFU per g soil were detected by dilution plating on a modified semiselective medium (SMSA). In comparison, a tomato bioassay was shown consistently to detect populations at or greater than 7·5 × 105 CFU per g soil. An indirect enzyme-linked immunosorbent assay (ELISA) was as sensitive as the tomato bioassay, but detected as few as 104 CFU per g soil when the suspension was first incubated in SMSA broth prior to testing. Detection using a nested polymerase chain reaction (PCR) was equally as sensitive as that using culture on SMSA agar, but only when the infested soil sample was first enriched overnight in SMSA broth prior to the nested PCR. Longer incubation periods in SMSA broth also increased the sensitivity of pathogen detection using a conventional PCR method, permitting detection of as few as 102 CFU per g soil after 60 h enrichment in SMSA broth. When evaluated using naturally infected field soils in Nepal, isolation of R. solanacearum on SMSA was reliable only when pathogen populations were higher than those of saprophytic soilborne bacteria. As few as 5 × 102 CFU of R. solanacearum per g were recovered from naturally infested soil, whereas the sensitivity of indirect ELISA was 106 CFU g,1. [source] soil-root-canopy interactionsANNALS OF APPLIED BIOLOGY, Issue 2 2001I J BINGHAM Summary When supplies of water and mineral nutrients are adequate, crop growth is determined by the amount of solar radiation intercepted over the season and the efficiency of its conversion into dry matter. Soil factors such as drought, nutrient availability, salinity, waterlogging, mechanical impedance and root-infecting pathogens can be a serious constraint to yield and operate through effects on the growth, photosynthetic activity and duration of the canopy, and on the partitioning of biomass to harvested parts. One approach to overcome restrictions on the canopy and enhance yield is to modify root systems so that they are better suited to the prevailing soil conditions. This might be achieved through genetic improvement or by cultural practices. A better understanding of the physiology of root systems is required to identify appropriate root traits for selection or management. Not only should this encompass considerations of the function of roots in the capture of water and nutrients and the provision of anchorage, but also new concepts about the role of chemical signals in the regulation of the canopy. Greater emphasis must be placed on field-based research. The growth, development and activity of roots in the field can differ markedly from those in most laboratory experiments, because field soils are more complex in structure and differ in their biological, chemical and physical properties. It is argued that a decline in field-based research of crop root systems, as seen in the UK over the last 15,20 years, could, if allowed to continue, generate a skills gap which may undermine future exploitation of discoveries made at the cell and molecular level. [source] | ||||||||||||||||||||||