scholarly journals Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction

2021 ◽  
Vol 9 (6) ◽  
pp. 1297
Author(s):  
Valentín Pérez-Hernández ◽  
Mario Hernández-Guzmán ◽  
Marco Luna-Guido ◽  
Yendi E. Navarro-Noya ◽  
Elda M. Romero-Tepal ◽  
...  
Keyword(s):  
Soil Salinity ◽  
Marker Gene ◽  
Lignocellulose Degradation ◽  
Alkaline Soil ◽  
Functional Prediction ◽  
Low Salinity ◽  
Soil Bacterial Community Structure ◽  
Maize Plants ◽  
Bacterial Groups ◽  
Taxonomic Annotation

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m−1, 17.3 dS m−1, and 33.4 dS m−1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m−1, 33.4 dS m−1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m−1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.

scholarly journals Calcium-Enriched Animal Manure Alleviates the Adverse Effects of Salt Stress on Growth, Physiology and Nutrients Homeostasis of Zea mays L.

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 480 ◽  
Author(s):  
Bushra Niamat ◽  
Muhammad Naveed ◽  
Zulfiqar Ahmad ◽  
Muhammad Yaseen ◽  
Allah Ditta ◽  
...  
Keyword(s):  
Nutrient Uptake ◽  
Soil Salinity ◽  
Crop Production ◽  
Growth Yield ◽  
Growth And Yield ◽  
Control Treatment ◽  
Soil Conditions ◽  
Alkaline Soil ◽  
Sodic Soil ◽  
Growth Physiology

Soil salinity and sodicity are among the main problems for optimum crop production in areas where rainfall is not enough for leaching of salts out of the rooting zone. Application of organic and Ca-based amendments have the potential to increase crop yield and productivity under saline–alkaline soil environments. Based on this hypothesis, the present study was conducted to evaluate the potential of compost, Ca-based fertilizer industry waste (Ca-FW), and Ca-fortified compost (Ca-FC) to increase growth and yield of maize under saline–sodic soil conditions. Saline–sodic soil conditions with electrical conductivity (EC) levels (1.6, 5, and 10 dS m−1) and sodium adsorption ratio (SAR) = 15, were developed by spiking soil with a solution containing NaCl, Na2SO4, MgSO4, and CaCl2. Results showed that soil salinity and sodicity significantly reduced plant growth, yield, physiological, and nutrient uptake parameters. However, the application of Ca-FC caused a remarkable increase in the studied parameters of maize at EC levels of 1.6, 5, and 10 dS m−1 as compared to the control. In addition, Ca-FC caused the maximum decrease in Na+/K+ ratio in shoot up to 85.1%, 71.79%, and 70.37% at EC levels of 1.6, 5, and 10 dS m−1, respectively as compared to the control treatment. Moreover, nutrient uptake (NPK) was also significantly increased with the application of Ca-FC under normal as well as saline–sodic soil conditions. It is thus inferred that the application of Ca-FC could be an effective amendment to enhance growth, yield, physiology, and nutrient uptake in maize under saline–sodic soil conditions constituting the novelty of this work.

Fidelity of a simple Liberty leaf-painting assay to validate transgenic maize plants expressing the selectable marker gene, bar

2017 ◽  
Vol 31 (4) ◽  
pp. 628-636 ◽  
Author(s):  
K. Rajasekaran ◽  
R. Majumdar ◽  
C. Sickler ◽  
Q. Wei ◽  
J. Cary ◽  
...  
Keyword(s):  
Selectable Marker ◽  
Marker Gene ◽  
Transgenic Maize ◽  
Selectable Marker Gene ◽  
Maize Plants

scholarly journals Lytic Bacteroides uniformis bacteriophages exhibiting host tropism congruent with diversity generating retroelement

2020 ◽  
Author(s):  
Stina Hedzet ◽  
Tomaž Accetto ◽  
Maja Rupnik
Keyword(s):  
Gut Microbiota ◽  
Outer Membrane Proteins ◽  
Marker Gene ◽  
Human Microbiome ◽  
Host Tropism ◽  
Sequence Variations ◽  
Common Marker ◽  
Evolutionary Advantage ◽  
Bacterial Groups

AbstractIntestinal phages are abundant and important component of gut microbiota, but our knowledge remains limited to only a few isolated and characterized representatives targeting numerically dominant gut bacteria. Here we describe isolation of human intestinal phages infecting Bacteroides uniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota, however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within Siphoviridae family and represent the first lytic phages, genomes of which encode diversity generating retroelements (DGR). This region is assumed to promote phage adaptation to the rapidly changing environmental conditions and to broaden its host range. Three isolated phages showed 99,83% genome identity but infected distinct B. uniformis strains. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% aa similarity to Bacuni phages in the genomes of B. acidifaciens and Prevotella sp.. Despite the abundance of Bacteroides within human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.ImportanceThe lack of common marker gene in viruses require a precise characterization of diverse isolated phages to enhance metagenomic analyses and to understand their role in gut microbiota. Here we report the isolation of phages representing a new genus with characteristics so far not known or rarely described in intestinal phages. They are the first lytic phages specific for Bacteroides uniformis, a bacterial representative of the prevalent genus in the gut of humans and animals. Additionally, they are the first lytic phages containing specific regions (diversity generating retroelement) that putatively influence host tropism. The ability to switch constantly the targeted populations of the host species could provide an evolutionary advantage to these bacteriophages and may affect intra species diversity.

scholarly journals Yield and ion content in maize irrigated with saline water in a continuous or alternating system

2012 ◽  
Vol 42 (10) ◽  
pp. 1731-1737 ◽  
Author(s):  
Felipe de Sousa Barbosa ◽  
Claudivan Feitosa de Lacerda ◽  
Hans Raj Gheyi ◽  
Gabriel Castro Farias ◽  
Ricardo José da Costa Silva Júnior ◽  
...  
Keyword(s):  
High Salinity ◽  
Saline Water ◽  
Block Design ◽  
Management Strategies ◽  
Growth Yield ◽  
Maize Yield ◽  
High Salinity Water ◽  
Low Salinity ◽  
Salinity Water ◽  
Maize Plants

Irrigation with water containing salt in excess can affect crop development. However, management strategies can be used in order to reduce the impacts of salinity, providing increased efficiency in the use of good quality water. The objective of this research was to study the effects of use of high salinity water for irrigation, in continuous or cyclic manner, on vegetative growth, yield, and accumulation of ions in maize plants. Two experiments were conducted during the months from October to January of the years 2008/2009 and 2009/2010, in the same area, adopting a completely randomized block design with four replications. Irrigation was performed with three types of water with electrical conductivities (ECw) of 0.8 (A1), 2.25 (A2) and 4.5 (A3) dS m-1, combined in seven treatments including the control with low salinity water (A1) throughout the crop cycle (T1). Saline waters (A2 and A3) were applied continuously (T2 and T5) or in a cyclic way, the latter being formed by six irrigations with A1 water followed by six irrigations by eitherA2 or A3 water, starting with A1 at sowing (T3 and T6) or 6 irrigations with A2 or A3 water followed by 6 irrigations with A1 water (T4 and T7) . The use of low and high salinity water resulted in lower accumulation of potentially toxic ions (Na and Cl) and improvement in the Na/K balance in the shoots of maize plants. Application of saline water in a cyclic way also allows the substitution of about 50% of water of low salinity in irrigation, without negative impacts on maize yield.

scholarly journals TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

2017 ◽  
Author(s):  
Ali Z Ijaz ◽  
Thomas Jeffries ◽  
Christopher Quince ◽  
Kelly Hamonts ◽  
Brajesh Singh
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Marker Gene ◽  
Evolutionary Conservation ◽  
Rrna Gene ◽  
Similarity Metric ◽  
Rdna Sequences ◽  
Fine Grain ◽  
16S Rdna Sequences ◽  
Taxonomic Annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.

scholarly journals Impact of Drought and Changing Water Sources on Water Use and Soil Salinity of Almond and Pistachio Orchards: 1. Observations

Soil Systems ◽  
2021 ◽  
Vol 5 (3) ◽  
pp. 50 ◽  
Author(s):  
Sarah A. Helalia ◽  
Ray G. Anderson ◽  
Todd H. Skaggs ◽  
G. Darrel Jenerette ◽  
Dong Wang ◽  
...  
Keyword(s):  
Soil Salinity ◽  
Irrigation Water ◽  
Root Zone ◽  
Temporal Distribution ◽  
Water Shortages ◽  
Low Salinity ◽  
Irrigation Water Salinity ◽  
Electrical Conductivities ◽  
Leaching Fraction ◽  
The Impact

Soil salinity increases when growers are forced to use higher salinity irrigation waters due to water shortages. It is necessary to estimate the impact of irrigation water on soil properties and conditions for crop growth to manage the effects of salinity on perennial crops. Therefore, in this study, we monitored root zone salinity in five almond and pistachio orchards in eastern and western San Joaquin Valley (SJV), California (CA). Volumetric soil water contents and bulk electrical conductivities were measured at four root-zone depths. Evapotranspiration was measured by eddy covariance along with three other types of data. The first is seasonal precipitation and irrigation patterns, including the temporal distribution of rains, irrigation events, and irrigation water salinity. The second is soil chemistry, including the initial sodium adsorption ratio (SAR) and soil solute electrical conductivity (ECe). The third type is the physical properties, including soil type, hydraulic conductivity, and bulk density. As expected, we found low salinity at the eastern sites and higher salinity at the western sites. The western sites have finer textured soils and lower quality irrigation water; measured actual ET was about 90% of modeled crop ET. Across the three western sites, the annual average apparent leaching fraction ranged from 11 to 28%. At the eastern sites, measured ET almost exactly matched modeled crop ET each year. Apparent leaching fractions in the eastern sites were approximately 20%.

scholarly journals Morphophysiological Traits of Gray Mangrove (Avicennia marina (Forsk.) Vierh.) at Different Levels of Soil Salinity

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Kholoud Abou Seedo ◽  
Mohammad S. Abido ◽  
Ahmed Salih ◽  
Asma Abahussain
Keyword(s):  
Electrical Conductivity ◽  
Soil Salinity ◽  
High Salinity ◽  
Avicennia Marina ◽  
The Other ◽  
Soil Electrical Conductivity ◽  
Pairwise Correlation ◽  
Positive Effects ◽  
Low Salinity ◽  
Different Levels

The traits of gray mangrove (Avicennia marina (Forsk.) Vierh.) at different levels of soil salinity were assessed at three sites along the Tubli Bay coastline of Bahrain. Morphophysiological traits include rates of photosynthesis and transpiration, leaf morphology, and leaf pigment content. Results showed that the rates of photosynthesis and transpiration, the intercellular CO2 concentration, and stomatal conductance were significantly lower (p ≤ 0.05) in the trees of a low salinity site compared to those of high salinity sites. Pairwise correlation between soil electrical conductivity levels and photosynthesis and transpiration rates was very low, implying an adverse effect of low salinity on both processes. However, the dimensions of leaf area and the sclerophylly index were significantly higher (p ≤ 0.05) in the trees grown in low salinity site compared to those in more saline conditions. On the other hand, pigments were significantly lower in leaves of trees grown in low salinity site compared to the other two sites. The pairwise correlation between electrical conductivity values and chlorophyll a, b, and carotenoid was 0.51, 0.52, and 0.57 consecutively at (p <0.0001), implying moderate effect of salinity on leaf pigments. This study illustrates the adverse and positive effects of soil salinity on some traits of gray mangrove in Bahrain, which might be considered in ecosystem rehabilitation along other coastlines of the country.

scholarly journals Soil Salinity Controls Relative Abundance of Specific Bacterial Groups Involved in the Decomposition of Maize Plant Residues

2018 ◽  
Vol 6 ◽  
Author(s):  
Arit S. De León-Lorenzana ◽  
Laura Delgado-Balbuena ◽  
Cristina A. Domínguez-Mendoza ◽  
Yendi E. Navarro-Noya ◽  
Marco Luna-Guido ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Soil Salinity ◽  
Maize Plant ◽  
Plant Residues ◽  
Bacterial Groups

scholarly journals TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

2017 ◽  
Author(s):  
Ali Z Ijaz ◽  
Thomas Jeffries ◽  
Christopher Quince ◽  
Kelly Hamonts ◽  
Brajesh Singh
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Marker Gene ◽  
Evolutionary Conservation ◽  
Rrna Gene ◽  
Similarity Metric ◽  
Rdna Sequences ◽  
Fine Grain ◽  
16S Rdna Sequences ◽  
Taxonomic Annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.

scholarly journals SENTINEL 2 AND LANDSAT-8 BANDS SENSITIVITY ANALYSIS FOR MAPPING OF ALKALINE SOIL IN NORTHERN DRY ZONE OF KARNATAKA, INDIA

2019 ◽  
Vol XLII-3/W6 ◽  
pp. 307-313 ◽  
Author(s):  
S. Meti ◽  
P. D. Lakshmi ◽  
M. S. Nagaraja ◽  
V. Shreepad ◽  
Keyword(s):  
High Resolution ◽  
Soil Ph ◽  
Satellite Data ◽  
Soil Salinity ◽  
Degradation Process ◽  
Landsat 8 ◽  
Alkaline Soil ◽  
Policy Makers ◽  
Dry Zone ◽  
Sentinel 2

<p><strong>Abstract.</strong> Soil salinization is most common land degradation process occurring in deep vertisol of northern dry zone of Karnataka, India. Accurate and high resolution spatial information on salinization can assist policy makers to better target areas for interventions to avoid aggravation of soil degradation process. Digital soil mapping using satellite data has been identified as a potential means of obtaining soil information. This paper focuses on exploring possibility of using new generation medium resolution Landsat-8 and Sentinel-2 satellite data to map alkaline soils of Ramthal irrigation project area in north Karnataka. Surface soil salinity parameters of zone 20 were correlated with reflectance values of different band and band combination and traditional salinity indices and result has indicated that SWIR bands of both satellite showed significant negative correlation with soil pH, EC (r&amp;thinsp;=&amp;thinsp;&amp;minus;0.39 to &amp;minus;0.45) whereas visible and NIR bands did not show significant relation. However rationing of SWIR bands with visible blue band has significantly improved the correlation with soil pH and EC (r&amp;thinsp;=&amp;thinsp;+0.60 to +0.70). Traditional salinity index based on visible bands failed to show significant correlation with soil parameters. It is interesting to note that SWIR bands alone did not show significant correlation with soil sodicity parameters like exchangeable Na, SAR, RSC but band rationing with blue bands has significantly improved the correlation (r&amp;thinsp;=&amp;thinsp;0.45). High resolution soil salinity map was prepared using simple linear regression model and using this map will serve as base map for the policy makers.</p>

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