A Microbiome Analysis of Soil Samples from Three Abandoned Lead-Silver Mines in the Arizona Sonoran Desert

2020 ◽  
Vol 49 (1) ◽  
Author(s):  
Daniel A. Lucas ◽  
Thomas M. Cahill ◽  
Pamela A. Marshall
Keyword(s):  
Sonoran Desert ◽  
Soil Samples ◽  
Microbiome Analysis

Harnessing the potential of the environmental microbiome in forensic science

2021 ◽  
pp. 61-67
Author(s):  
Agata Jagiełło ◽  
◽  
Anna Woźniak ◽  
Błażej Szczerba ◽  
Rafał Płoski ◽  
...  
Keyword(s):  
Forensic Science ◽  
Dna Analysis ◽  
Genetic Test ◽  
Massively Parallel Sequencing ◽  
Geographical Location ◽  
Soil Samples ◽  
Massively Parallel ◽  
Soil Microbiome ◽  
Microbiome Analysis ◽  
Dna Profiles

A scientific consortium led by the Central Forensic Laboratory of the Police has undertaken to develop a method for DNA analysis of the soil microbiome to be used in forensic investigations. The aim of the project entitled Soil Microbiome Analysis Forensic Tool – SMAFT (http://smaft.eu/), financed by the National Center for Research and Development (DOB-BIO10/03/01/2019), is to develop a new tool that enables the association of a trace in the form of a soil sample with a specific geographical location. The first part of the paper introduces the concept of the microbiome and presents the possibilities of using microbiome DNA analysis in forensic science. In the second part, the stages of the SMAFT project are described in detail, beginning from the collection of soil samples from different sites in Poland across all seasons and isolation of microbiome DNA through massively parallel sequencing (MPS) technology-based analysis of isolates and the development of a genetic test containing a set of metagenomic markers allowing for effective individualization of soil samples, up to the creation of an IT system enabling analysis and interpretation of the obtained results, which includes a database of soil microbiome DNA profiles from various locations in Poland.

scholarly journals Microbiome Analysis of the Rhizosphere from Wilt Infected Pomegranate Reveals Complex Adaptations in Fusarium—A Preliminary Study

Agriculture ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 831
Author(s):  
Anupam J. Das ◽  
Renuka Ravinath ◽  
Talambedu Usha ◽  
Biligi Sampgod Rohith ◽  
Hemavathy Ekambaram ◽  
...  
Keyword(s):  
Early Stage ◽  
Soil Nutrient ◽  
Intermediate Stage ◽  
Rapid Identification ◽  
Wilt Disease ◽  
Soil Samples ◽  
Carbohydrate Binding ◽  
Microbiome Analysis ◽  
Metagenome Sequencing ◽  
Achromobacter Sp

Wilt disease affecting pomegranate crops results in rapid soil-nutrient depletion, reduced or complete loss in yield, and crop destruction. There are limited studies on the phytopathogen Fusarium oxysporum prevalence and associated genomic information with respect to Fusarium wilt in pomegranate. In this study, soil samples from the rhizosphere of different pomegranate plants showing early stage symptoms of wilt infection to an advanced stage were collected from an orchard situated in Karnataka, India. A whole metagenome sequencing approach was employed to gain insights into the adaptations of the causative pathogen F. oxysporum. Physicochemical results showed a drop in the pH levels, N, Fe, and Mn, and increase in electrical conductivity, B, Zn, Cl, Cu was observed in the early and intermediate stage samples. Comparative abundance analysis of the experimental samples ESI and ISI revealed an abundance of Proteobacteria phyla Achromobacter sp. 2789STDY5608625, Achromobacter sp. K91, and Achromobacter aegrifaciens and Eukaryota namely Aspergillus arachidicola, Aspergillus candidus, and Aspergillus campestris. Functional pathway predictions implied carbohydrate binding to be significant (p < 0.05) among the three experimental samples. Microbiological examination and whole microbiome analysis confirmed the prevalence of F. oxysporum in the soil samples. Variant analysis of F. oxysporum revealed multiple mutations in the 3IPD gene with high impact effects. 3-Isopropylmalate dehydratase and carbohydrate-active enzymes could be good targets for the development of antifungals that could aid in biocontrol of F. oxysporum. The present study demonstrates the capabilities of the whole metagenome sequencing approach for rapid identification of potential key players of wilt disease pathogenesis wherein the symptomatology is complex.

K-MEANS CLUSTERING ALGORITHM BASED CLASSIFICATION OF SOIL FERTILITY IN NORTH WEST NIGERIA

2020 ◽  
Vol 4 (2) ◽  
pp. 780-787
Author(s):  
Ibrahim Hassan Hayatu ◽  
Abdullahi Mohammed ◽  
Barroon Ahmad Isma’eel ◽  
Sahabi Yusuf Ali
Keyword(s):  
Soil Fertility ◽  
Crop Yield ◽  
Clustering Algorithm ◽  
Soil Samples ◽  
North West ◽  
R Programming ◽  
Available Information ◽  
Northwest Region ◽  
The Relationship

Soil fertility determines a plant's development process that guarantees food sufficiency and the security of lives and properties through bumper harvests. The fertility of soil varies according to regions, thereby determining the type of crops to be planted. However, there is no repository or any source of information about the fertility of the soil in any region in Nigeria especially the Northwest of the country. The only available information is soil samples with their attributes which gives little or no information to the average farmer. This has affected crop yield in all the regions, more particularly the Northwest region, thus resulting in lower food production.  Therefore, this study is aimed at classifying soil data based on their fertility in the Northwest region of Nigeria using R programming. Data were obtained from the department of soil science from Ahmadu Bello University, Zaria. The data contain 400 soil samples containing 13 attributes. The relationship between soil attributes was observed based on the data. K-means clustering algorithm was employed in analyzing soil fertility clusters. Four clusters were identified with cluster 1 having the highest fertility, followed by 2 and the fertility decreases with an increasing number of clusters. The identification of the most fertile clusters will guide farmers on where best to concentrate on when planting their crops in order to improve productivity and crop yield.

Characterization of dissolved organic matter (DOM) extracted from soils by hot water percolation (HWP)

2010 ◽  
Vol 59 (1) ◽  
pp. 99-108 ◽  
Author(s):  
M. Takács ◽  
Gy. Füleky
Keyword(s):  
Organic Matter ◽  
Humic Acid ◽  
Natural Organic Matter ◽  
Extraction Methods ◽  
Soil Samples ◽  
Hot Water ◽  
Soil Extracts ◽  
Water Percolation ◽  
Soil Humic Acid

The Hot Water Percolation (HWP) technique for preparing soil extracts has several advantages: it is easily carried out, fast, and several parameters can be measured from the same solution. The object of this study was to examine the possible use of HWP extracts for the characterization of soil organic matter. The HPLC-SEC chromatograms, UV-VIS and fluorescence properties of the HWP extracts were studied and the results were compared with those of the International Humic Substances Society (IHSS) Soil Humic Acid (HA), IHSS Soil Fulvic Acid (FA) and IHSS Suwannee Natural Organic Matter (NOM) standards as well as their HA counterparts isolated by traditional extraction methods from the original soil samples. The DOM of the HWP solution is probably a mixture of organic materials, which have some characteristics similar to the Soil FA fractions and NOM. The HWP extracted organic material can be studied and characterized using simple techniques, like UV-VIS and fluorescence spectroscopy.

Soil response to chemicals used in a field experiment

2013 ◽  
Vol 27 (2) ◽  
pp. 151-158 ◽  
Author(s):  
S. Jezierska-Tys ◽  
A. Rutkowska
Keyword(s):  
Alkaline Phosphatase ◽  
Enzymatic Activity ◽  
Field Experiment ◽  
Soil Microorganisms ◽  
Block Design ◽  
Soil Samples ◽  
Alkaline Phosphatases ◽  
Soil Response ◽  
Negative Effect ◽  
Set Up

Abstract The effect of chemicals (Reglone 200 SL and Elastiq 550 EC) on soil microorganisms and their enzymatic activity was estimated. The study was conducted in a field experiment which was set up in the split-block design and comprised three treatments. Soil samples were taken six times, twice in each year of study. The results showed that the application of chemicals generally had no negative effect on the number of soil microorganisms. The application of Reglone 200 SL caused an increase of proteolytic and ureolytic activity and affected the activity of dehydrogenases, acid and alkaline phosphatases in the soil. The soil subjected of Elastiq 550 EC was characterized by lower activity of dehydrogenases, protease, urease and alkaline phosphatase.

Sidrophore Production and Phosphate Solubilization by Bacillus cereus and Pseudomonas fluorescens Isolated from Iraqi Soils and Soil Characterization

2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Zaid Raad Abbas ◽  
Aqeel Mohammed Majeed Al-Ezee ◽  
Sawsan H
Keyword(s):  
Bacillus Cereus ◽  
Pseudomonas Fluorescens ◽  
Phosphate Solubilization ◽  
Bacterial Species ◽  
Nutrient Status ◽  
Bacterial Count ◽  
Soil Samples ◽  
Phosphate Solubilizing Bacteria ◽  
Clear Zone ◽  
Zone Formation

This study was conducted to explore the ability of Pseudomonas fluorescens and Bacillus cereus to solubilizing a phosphate in soil for enhancing the planting growth and, its relation with soill characterization. The isolates were identified as P.fluorescens and B. cereus using convential analysis and, its phosphate solubilization ability and sidrophore was shown by the clear zone formation on National Botanical Research Institute���s Phosphate medium. Moreover, Pseudomonas fluorescens isolates (n = 9) and three of B. cereus isolated from agricultural area in Baghdad university, Mustansiriyah university and Diyala bridge. Results displayed that bacterial count were varied in soil samples according to their region, and ranging from 30 to 60 *10 2 CFU/g in Baghdad university soil to 10���20 *10 2 CFU/g in Mustansiriyah university soil, the Baghdad soil macronutrient which included: NH4, NO3, P, and K were, 8.42, 20.53, 19.09, 218.73 respectively, While the physio analysis revealed that the mean of pH was 7.3 and EC was 8.63. on the other hand the micronutrient analysis indicated that the soil samples were included Ca, Fe, Mn, Zn and Cu which gave their mean 5025.9, 8.9, 4.9, 0.5 and 1.5 respectevily. Results revealed that all isolated bacteria (9 isolates of P.fluorescens and three isolates of B. cereus gave ahalo zone which mean their ability to be phosphate solubilizing bacteria at 100%. Results revealed that all isolated bacteria were detected a ability to produce high levels from chelating agents (siderophores)) by P.fluorescens and. B cereus at 100%, when appeared ahalo clear zone. Furthermore, the high levels of phosphate solubilization and siderophore production were grouped in bacterial species isolated from Iraqi soils. might be attributed to many soil factors such as soil nutrient status, soil acidity, water content, organic matter and soil enzyme activities.

Sign in / Sign up

Export Citation Format

Share Document