EVALUATION OF DIFFERENT TECHNIQUES FOR DNA DIRECT EXTRACTION FROM BRAZILIAN AGRICULTURAL SOIL

Soil is an ecosystem characterized by a great complexity and hard to study due to its heterogeneity, especially the soil microorganism’s community. Currently, molecular biology tools have been used to study the soil biodiversity mainly through microbial genes. DNA Direct Extraction from soil is an important step in this kind of study, however the majority of techniques were developed for soils from temperate climate and just a few can be applied efficiently to Brazilian soils. This work aimed to evaluate nine different techniques for soil DNA direct extraction from sugarcane crop areas under organic and conventional managements and also to propose modifications which might result in higher DNA yield and low cost. DNA bands were observed only for three techniques (Selbach´s, Direito´s and commercial kit), two of them already tested for tropical climate soils. The best results for DNA yield (µg.g-1 soil) were obtained through Selbach´s and commercial kit techniques, however not differing statistically from those results through a protocol here proposed. This modified protocol showed the best results for DNA yield whatever soil was used. The best DNA yields were found in soil under organic management probably due to higher microbial biomass. This protocol showed better results in yield of DNA regardless of the soil used and was easier to perform and less costly.

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Sodium Alginate versus Plasma Thrombin Cell Blocks in Diagnostic Cytopathology: A Comparative Analysis

Acta Cytologica ◽

10.1159/000519336 ◽

2021 ◽

pp. 1-7

Author(s):

Shruti Gupta ◽

Upasana Gautam ◽

Shaily Susheilia ◽

Baneet Bansal ◽

Radha Uppal ◽

...

Keyword(s):

Sodium Alginate ◽

Molecular Analysis ◽

Low Cost ◽

Nuclear Marker ◽

Fine Needle Aspirates ◽

Dna Yield ◽

Morphological Evaluation ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Formalin Fixed

Background: Cell blocks (CBs) are an essential adjunct in cytopathology practice. The aim of this study was to compare 2 techniques of CB preparation – plasma thrombin (PT) method with sodium alginate (SA) method for overall cellularity, morphological preservation, obscuring artefacts, immunocytochemistry (ICC), suitability for molecular analysis, and cost of preparation. Design: A total of 80 fine-needle aspirates from various sites and serous effusion samples were included. Of these cases, by random selection, 40 each were prepared by PT method and SA methods, respectively. The haematoxylin-eosin-stained sections from the formalin-fixed, paraffin-embedded CBs from both methods were evaluated in a blinded fashion by 2 cytopathologists and scored for cellularity, artefacts, and morphological preservation and analysed by χ2 test with Yates correction. We evaluated 6 cases from each method by ICC for a range of membrane, cytoplasmic and nuclear marker expression. DNA was extracted from four cases to evaluate their utility for molecular analysis. Results: CB sections from PT and SA techniques showed comparable cellularity and excellent cytomorphological preservation. Blue gel-like artefacts were common in the SA technique but did not interfere with morphological evaluation. ICC staining results were also similar. DNA yield and utility for PCR were also comparable. The SA-CB cost half that of PT-CB (USD 0.4 vs. USD 1). Conclusion: SA technique of CB preparation is an excellent low-cost alternative to PT method for CB preparation.

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Radiosity from Individual Urban Landscape Elements Measured Using a Modified Low-Cost Temperature Sensor

Urban Science ◽

10.3390/urbansci4010014 ◽

2020 ◽

Vol 4 (1) ◽

pp. 14

Author(s):

Jane Loveday ◽

Grant K. Loveday ◽

Joshua J. Byrne ◽

Boon-lay Ong ◽

Gregory M. Morrison

Keyword(s):

Urban Landscape ◽

Low Cost ◽

Local Environment ◽

Weather Conditions ◽

Temperate Climate ◽

View Factor ◽

Heat Management ◽

Landscape Elements ◽

Urban Heat ◽

Warm Temperate

Loss of green space in our suburban environment is contributing to increased urban heat. The material properties of surface treatments or landscape elements (LEs) are a determining factor in the amount, timing, and type of radiation present in the local environment. Landscape designers can use this information to better design for urban heat management, as emitted and reflected radiation (radiosity) from LEs can affect pedestrians via heat stress and glare and affect energy usage in buildings and houses if the landscape sky view factor is low. Low-cost black painted iButton temperature sensors were successfully used as radiometers to concurrently measure the daytime radiosity from 19 LEs samples located on an oval in the warm temperate climate of Perth, (Australia). Normalisation against gloss white paint on polystyrene removed the effect of varying weather conditions. Each LE had the same normalised average radiosity (DRav) between seasons (within ±5%), meaning the relative radiosity of new LEs can be measured on any day. White and lighter coloured LEs had the highest DRav and would have the most detrimental effect on nearby objects. Plants and moist LEs had the least DRav and would be most beneficial for managing local daytime urban heat. Measuring relative radiosity with iButtons presents a new way to examine the effect of LEs on the urban environment.

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Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils

Canadian Journal of Microbiology ◽

10.1139/w11-049 ◽

2011 ◽

Vol 57 (8) ◽

pp. 623-628 ◽

Cited By ~ 42

Author(s):

Nagissa Mahmoudi ◽

Greg F. Slater ◽

Roberta R. Fulthorpe

Keyword(s):

Dna Extraction ◽

Contaminated Soils ◽

Dna Isolation ◽

Extraction Process ◽

Organic Carbon Content ◽

Soil Dna ◽

Isolation And Purification ◽

Dna Yield ◽

Pcr Products ◽

Eukaryotic Dna

Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid–liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.

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Intraurban Temperature Variability in Baltimore

Journal of Applied Meteorology and Climatology ◽

10.1175/jamc-d-16-0232.1 ◽

2017 ◽

Vol 56 (1) ◽

pp. 159-171 ◽

Cited By ~ 10

Author(s):

Anna A. Scott ◽

Ben Zaitchik ◽

Darryn W. Waugh ◽

Katie O’Meara

Keyword(s):

Surface Properties ◽

Land Surface ◽

Low Cost ◽

Canopy Cover ◽

Tree Canopy ◽

Temperate Climate ◽

Weather Station ◽

Underserved Area ◽

Air Temperatures ◽

Tree Canopy Cover

AbstractHow much does minimum daily air temperature vary within neighborhoods exhibiting high land surface temperature (LST), and does this variability affect agreement with the nearest weather station? To answer these questions, a low-cost sensor network of 135 “iButton” thermometers was deployed for summer 2015 in Baltimore, Maryland (a midsized American city with a temperate climate), focusing on an underserved area that exhibits high LST from satellite imagery. The sensors were evaluated against commercial and NOAA/NWS stations and showed good agreement for daily minimum temperatures. Variability within the study site was small: mean minimum daily temperatures have a spatial standard deviation of 0.9°C, much smaller than the same measure for satellite-derived LST. The sensor-measured temperatures agree well with the NWS weather station in downtown Baltimore, with a mean difference for all measurements in time and space of 0.00°C; this agreement with the station is not found to be correlated with any meteorological variables with the exception of radiation. Surface properties are found to be important in determining spatial variability: vegetated or green spaces are observed to be 0.5°C cooler than areas dominated by impervious surfaces, and the presence of green space is found to be a more significant predictor of temperature than surface properties such as elevation. Other surface properties—albedo, tree-canopy cover, and distance to the nearest park—are not found to correlate significantly with air temperatures.

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Soil quality - Direct extraction of soil DNA

10.3403/30265376u ◽

2020 ◽

Keyword(s):

Soil Quality ◽

Direct Extraction ◽

Soil Dna

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DNA Extraction from Soils: Old Bias for New Microbial Diversity Analysis Methods

Applied and Environmental Microbiology ◽

10.1128/aem.67.5.2354-2359.2001 ◽

2001 ◽

Vol 67 (5) ◽

pp. 2354-2359 ◽

Cited By ~ 459

Author(s):

F. Martin-Laurent ◽

L. Philippot ◽

S. Hallet ◽

R. Chaussod ◽

J. C. Germon ◽

...

Keyword(s):

Dna Extraction ◽

Ribosomal Dna ◽

Dna Analysis ◽

Restriction Analysis ◽

Farmyard Manure ◽

Soil Biodiversity ◽

Soil Dna ◽

Recovery Method ◽

Dna Recovery ◽

The Impact

ABSTRACT The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.

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Evaluation of Soil DNA from Arable Land in Japan Using a Modified Direct-extraction Method

Microbes and Environments ◽

10.1264/jsme2.19.301 ◽

2004 ◽

Vol 19 (4) ◽

pp. 301-309 ◽

Cited By ~ 31

Author(s):

Seishi Ikeda ◽

Kazuo N. Watanabe ◽

Kiwamu Minamisawa ◽

Nozomi Ytow

Keyword(s):

Extraction Method ◽

Arable Land ◽

Direct Extraction ◽

Soil Dna

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Dry season and soil texture affect the chemical control of monocotyledonous in sugarcane

Comunicata Scientiae ◽

10.14295/cs.v8i3.1594 ◽

2018 ◽

Vol 8 (3) ◽

pp. 477-485

Author(s):

Hudson Kagueyama Takano ◽

Denis Fernando Biffe ◽

Jamil Constantin ◽

Rubem Silvério de Oliveira Junior ◽

Guilherme Braga Pereira Braz ◽

...

Keyword(s):

Soil Texture ◽

Rainy Season ◽

Clayey Soil ◽

Dry Season ◽

Weed Species ◽

Wet Season ◽

Sugarcane Crop ◽

Dry Conditions ◽

Loam Soil ◽

Great Complexity

The chemical weed control in sugarcane during the wet season is more effective than the control carried out during the dry season. The objective of this study was to evaluate the efficacy of herbicides in the rainy season and in the dry season in sugarcane crop, and in different soil textural classes. The experiments simulated dry season and rainy season basing on periods of days in which experiment was submitted to irrigation restriction. In each experiment, it was tested 50 and 100% of the dose of the main herbicides commonly used in sugarcane to control B. decumbens, B. plantaginea, P. maximum and D. horizontalis. In general, in dry conditions, as well as varying the soil texture, there are restrictions in the choice of herbicide to be used due to the reduced effectiveness of some treatments in certain situations. In the very-clayey soil, especially in the dry season, the efficacy of herbicides is better, whereas, for the sandy-clay-loam soil in dry conditions, the effectiveness of herbicides is restricted. Thus, this study, despite the great complexity of the variables to be analyzed, permitted to establish guidelines for decision making on the most appropriate herbicide to be applied in each studied condition, in order to control these weed species.

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Effects of agricultural soil management practices on soil microbiota across Europe – investigations in seven long term field experiments

10.5194/egusphere-egu2020-11299 ◽

2020 ◽

Author(s):

Luis F. Arias ◽

Gema Guzmán ◽

José A. Gómez ◽

Manuel Anguita-Maeso ◽

Dumitria Dascalu ◽

...

Keyword(s):

Ecosystem Services ◽

Beta Diversity ◽

Alpha Diversity ◽

Soil Management ◽

Soil Biota ◽

Fungal Communities ◽

Soil Biodiversity ◽

Soil Dna ◽

General Terms

Traditionally, soil quality has been assessed through physical, chemical and biological properties without paying attention to soil biota and the different associated ecosystem services provided (Tyler, 2019). To fill that gap, the european BiodivERsA &#8220;SoilMan&#8221; project (Ecosystem services driven by the diversity of soil biota &#8211; understanding and management in agriculture) is focused on the relations among soil management, soil biodiversity, and ecosystem services, at seven different management gradients in agricultural long term observations (LTO&#8217;s) trials across Europe (France &#8220;SOERE-PROs EFELE&#8221; and &#8220;SOERE-ACBB Lusigan&#8221;, Romania &#8220;Turda&#8221;, Sweden &#8220;Angermanland&#8221; and &#8220;S&#228;by-Uppland&#8221;, Germany &#8220;Garte S&#252;d&#8221; and Spain &#8220;La Hampa&#8221;). Management gradients covered different tillage regimes (zero, minimum and conventional) and different crop rotations (crop types and duration).In the present study, we characterised the bacterial and fungal communities of soils from the different countries and agricultural managements in arable land. The samplings were carried out following the same methodology in all the countries during 2017-2018 when wheat was sown in the LTO&#8217;s. The soil DNA was extracted and subjected to metabarcoding analysis of 16S and Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) for bacterial and fungal community analysis, respectively.Different alpha diversity metrics, including number of OTUs, Simpsons and Shannon indexes, as well as beta diversity distances (weighted and unweighted UNIFRAC, Jaccard and Bray-Curtis) were calculated. Multidimensional Scaling ordination plots (PCoA) were used to visualize the existence of community gradients among locations and soil managements. All the statistical data&#160; procedure&#160; was analysed using the vegan R package (Oksanen, 2011).In general terms, results show that alpha diversity for both bacteria and fungi, clearly differs among countries while soil management effects are less defined among and within countries. Concerning the beta diversity indexes, communities tend to cluster more according to the spatial location than due to the soil management regimen. This is especially true for fungal communities. Further analysis will identify possible correlations of bacterial and fungal communities with environmental variables and other physicochemical and biological soil properties.References:Oksanen, J. (2011). Multivariate Analysis of Ecological Communities in R: vegan tutorial.Tyler, H. L. (2019). Bacterial community composition under long-term reduced tillage and no till management. Journal of Applied Microbiology, 126(6), 1797&#8211;1807. https://doi.org/10.1111/jam.14267

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Effects of different litter depths on environmental parameters and growth performance of growing finishing pigs

Ciência Rural ◽

10.1590/s0103-84782008005000094 ◽

2008 ◽

Vol 39 (3) ◽

pp. 838-843 ◽

Cited By ~ 7

Author(s):

Érico Kunde Corrêa ◽

Ivan Bianchi ◽

Rafael da Rosa Ulguim ◽

Marcio Nunes Corrêa ◽

Carlos Gil-Turnes ◽

...

Keyword(s):

Relative Humidity ◽

Thermal Comfort ◽

Growth Performance ◽

Low Cost ◽

Environmental Parameters ◽

Atmospheric Temperature ◽

Feed Consumption ◽

Temperate Climate ◽

Finishing Pigs ◽

T1 And T2

Deep litter systems represent low cost alternatives to raise growing-finishing pigs, reducing slurry accumulation, although pig's thermal comfort may be negatively affected by the heat produced inside the litter. This study compared environmental and performance parameters for growing-finishing pigs raised on deep litter systems having distinct depths and on solid floor. The experiment was conducted in a region of temperate climate of Brazil, comparing three treatments: litter having rice husk 0.5m (T1); and 0.25m deep (T2); and solid concrete floor (T3). The first litter was used in two lots and replaced by a second litter used in other two lots, during 52 weeks. Each lot included five pigs in a 7m² pen, from 60 to 145 d of age. Environmental parameters were determined at weekly intervals, including: atmospheric temperature; relative humidity; temperature at the center of the pen, in the surface (TSF); and at half of the depth (THD), only for T1 and T2. Feed consumption and weight of pigs were measured every four weeks. Atmospheric temperature and relative humidity were not influenced by the treatments (P>0.05). Mean TSF was 22.8 ± 3.6°C, being lower for T3 (P<0.05), but with no difference between T1 and T2 (P>0.05). TSF was higher for new than for used litters (P<0.001) and for the first than for the second litter (P=0.03), apparently increasing in lots raised during termophilic phases. Mean THD was 33.8±10.8°C, being higher for T1 than for T2 (P<0.05). THD was also higher for new than for used litters (P<0.001) and for the first than for the second litters (P<0.05). No growth performance parameter differed across treatments (P>0.05). Despite the potential unfavorable thermal comfort under high temperatures, deep litter systems can be used to raise pigs in the growing-finishing phases due to the absence of negative effects for growth performance.

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