scholarly journals NMR-Based Metabolomic Analysis and Microbial Composition of Soil Supporting Burkea africana Growth

Metabolites ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 402
Author(s):  
Lufuno Ethel Nemadodzi ◽  
Jacques Vervoort ◽  
Gerhard Prinsloo
Keyword(s):  
Mass Spectrometry Analysis ◽  
Metabolomic Analysis ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Penicillium Species ◽  
Bacterial Composition ◽  
Spectrometry Analysis ◽  
Soil Microbial ◽  
Natural Establishment ◽  
Survival Of Seedlings

Burkea africana is a leguminous tree used for medicinal purposes, growing in clusters, on soils impoverished from most nutrients. The study aimed to determine the factors responsible for successful reproduction and establishment of the B. africana trees in nature, as all efforts for commercial production has been proven unsuccessful. An investigation was carried out to determine the metabolomic profile, chemical composition, and microbial composition of the soils where B. africana grows (Burkea soil) versus the soil where it does not grow (non-Burkea soil). 1H-NMR metabolomic analysis showed different metabolites in the respective soils. Trehalose and betaine, as well as a choline-like and carnitine-like compound, were found to be in higher concentration in Burkea soils, whereas, acetate, lactate, and formate were concentrated in non-Burkea soils. Liquid Chromatography-Mass Spectrometry analysis revealed the presence of numerous amino acids such as aspartic acid and glutamine to be higher in Burkea soils. Since it was previously suggested that the soil microbial diversity is the major driver for establishment and survival of seedlings in nature, Deoxyribonucleic acid (DNA) was extracted and a BLAST analysis conducted for species identification. Penicillium species was found to be highly prevalent and discriminant between the two soils, associated with the Burkea soils. No differences in the bacterial composition of Burkea and non-Burkea soils were observed. The variances in fungal composition suggests that species supremacy play a role in development of B. africana trees and is responsible for creating a supporting environment for natural establishment and survival of seedlings.

scholarly journals Positive effects of crop diversity on productivity driven by changes in soil microbial composition

2020 ◽  
Author(s):  
Laura Stefan ◽  
Martin Hartmann ◽  
Nadine Engbersen ◽  
Johan Six ◽  
Christian Schöb
Keyword(s):  
Plant Growth ◽  
Microbial Diversity ◽  
Crop Yield ◽  
Soil Microbial Communities ◽  
Crop Diversity ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Positive Effects ◽  
Soil Microbial Composition

SummaryIntensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and functions, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (3 times larger) or soil moisture (3 times larger). Furthermore, these processes were context-dependent: in Spain, where soil resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes, thereby emphasizing the context-dependence of crop–microbe relationships.

scholarly journals Positive Effects of Crop Diversity on Productivity Driven by Changes in Soil Microbial Composition

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Stefan ◽  
Martin Hartmann ◽  
Nadine Engbersen ◽  
Johan Six ◽  
Christian Schöb
Keyword(s):  
Plant Growth ◽  
Microbial Diversity ◽  
Crop Yield ◽  
Soil Microbial Communities ◽  
Crop Diversity ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Positive Effects ◽  
Soil Microbial Composition

Intensive agriculture has major negative impacts on ecosystem diversity and functioning, including that of soils. The associated reduction of soil biodiversity and essential soil functions, such as nutrient cycling, can restrict plant growth and crop yield. By increasing plant diversity in agricultural systems, intercropping could be a promising way to foster soil microbial diversity and functioning. However, plant–microbe interactions and the extent to which they influence crop yield under field conditions are still poorly understood. In this study, we performed an extensive intercropping experiment using eight crop species and 40 different crop mixtures to investigate how crop diversity affects soil microbial diversity and activity, and whether these changes subsequently affect crop yield. Experiments were carried out in mesocosms under natural conditions in Switzerland and in Spain, two countries with drastically different soils and climate, and our crop communities included either one, two or four species. We sampled and sequenced soil microbial DNA to assess soil microbial diversity, and measured soil basal respiration as a proxy for soil activity. Results indicate that in Switzerland, increasing crop diversity led to shifts in soil microbial community composition, and in particular to an increase of several plant-growth promoting microbes, such as members of the bacterial phylum Actinobacteria. These shifts in community composition subsequently led to a 15 and 35% increase in crop yield in 2 and 4-species mixtures, respectively. This suggests that the positive effects of crop diversity on crop productivity can partially be explained by changes in soil microbial composition. However, the effects of crop diversity on soil microbes were relatively small compared to the effects of abiotic factors such as fertilization (three times larger) or soil moisture (three times larger). Furthermore, these processes were context-dependent: in Spain, where resources were limited, soil microbial communities did not respond to crop diversity, and their effect on crop yield was less strong. This research highlights the potential beneficial role of soil microbial communities in intercropping systems, while also reflecting on the relative importance of crop diversity compared to abiotic drivers of microbiomes and emphasizing the context-dependence of crop–microbe relationships.

scholarly journals Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2459 ◽  
Author(s):  
Silvia Pajares ◽  
Ana E. Escalante ◽  
Ana M. Noguez ◽  
Felipe García-Oliva ◽  
Celeste Martínez-Piedragil ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Spatial Heterogeneity ◽  
Abiotic Factors ◽  
Soil Microbial Communities ◽  
Arid Ecosystems ◽  
Arid Soils ◽  
Chemical Parameters ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO${}_{3}^{-}$, Cl−, SO${}_{4}^{2-}$) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

scholarly journals Impacts of Chlorpyrifos and Deltamethrin on Soil Bacterial Community Composition in Different Salinity Soils: Natural Attenuation Microcosm Studies

2021 ◽  
Author(s):  
Safoura Hashemi Jokar ◽  
Mahmoud Shavandi ◽  
Azam Haddadi ◽  
Ebrahim Alaie
Keyword(s):  
Natural Attenuation ◽  
Saline Soil ◽  
Bacterial Community Composition ◽  
Saline Control ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Agricultural Industry ◽  
Soil Microbial ◽  
Control Microcosm ◽  
Negative Impacts

Abstract Pesticides and insecticides are the chemicals widely used in the agricultural industry, but their ecotoxicological effects on the environment are not still well understood. In this study, the remediation of chlorpyrifos (CP) and deltamethrin (DM) and their impacts on soil microbial diversity was investigated. Four different soils with various salinity (0%, 1%, 2% and 4%) were artificially contaminated by CP and DM. Then, natural attenuation of the pesticides in soil microcosms and their effects on soil microbial composition were studied by metagenomics. The pesticide natural attenuation analysis showed higher CP remediation in slightly saline soils with 1% and 2% salinity and faster removal of DM in 1% saline soil in comparison to non-saline control microcosm. The complete natural attenuation of the contaminants took around 60 days. The metagenomics analysis indicated that pesticide contamination had significant impacts on the soil flora and some dominant species in the control microcosm were completely eliminated by CP and DM. In addition, Paenibacillus (2% salinity and DM), Bacillus (4% salinity and CP), Paeniclostridium (1% salinity and DM) and Lachnospiraceae (1% salinity and CP) were the dominant genus by 77%, 50%, 41% and 39% relative abundances, respectively. At phylum level, the sequences belonged to Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were considerably enriched during natural attenuation of both DM and CP pesticides. Furthermore, Shannon and Simpson Indexes were identified more sensitive to the microbial community evenness, while, Chao1 and ACE indexes were changed by the community abundance. It was revealed that the highest negative impacts of deltamethrin and chlorpyrifos on the culturable and unculturable communities were related to the non-saline soil.

scholarly journals Intercropping Alters the Soil Microbial Diversity and Community to Facilitate Nitrogen Assimilation: A Potential Mechanism for Increasing Proso Millet Grain Yield

2020 ◽  
Vol 11 ◽  
Author(s):  
Ke Dang ◽  
Xiangwei Gong ◽  
Guan Zhao ◽  
Honglu Wang ◽  
Aliaksandr Ivanistau ◽  
...  
Keyword(s):  
Grain Yield ◽  
Microbial Diversity ◽  
Mung Bean ◽  
Rhizosphere Soil ◽  
Potential Mechanism ◽  
Microbial Composition ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Proso Millet ◽  
N Assimilation

Intercropping of cereals and legumes has been used in modern agricultural systems, and the soil microorganisms associated with legumes play a vital role in organic matter decomposition and nitrogen (N) fixation. This study investigated the effect of intercropping on the rhizosphere soil microbial composition and structure and how this interaction affects N absorption and utilization by plants to improve crop productivity. Experiments were conducted to analyze the rhizosphere soil microbial diversity and the relationship between microbial composition and N assimilation by proso millet (Panicum miliaceum L.) and mung bean (Vigna radiata L.) from 2017 to 2019. Four different intercropping row arrangements were evaluated, and individual plantings of proso millet and mung bean were used as controls. Microbial diversity and community composition were determined through Illumina sequencing of 16S rRNA and internal transcribed spacer (ITS) genes. The results indicated that intercropping increased N levels in the soil–plant system and this alteration was strongly dependent on changes in the microbial (bacterial and fungal) diversities and communities. The increase in bacterial alpha diversity and changes in unique operational taxonomic unit (OTU) numbers increased the soil N availability and plant N accumulation. Certain bacterial taxa (such as Proteobacteria) and fungal taxa (such as Ascomycota) were significantly altered under intercropping and showed positive responses to increased N assimilation. The average grain yield of intercropped proso millet increased by 13.9–50.1% compared to that of monoculture proso millet. Our data clearly showed that intercropping proso millet with mung bean altered the rhizosphere soil microbial diversity and community composition; thus, this intercropping system represents a potential mechanism for promoting N assimilation and increasing grain yield.

scholarly journals Metabolomic analysis of skeletal muscle before and after strenuous exercise to fatigue

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hajime Ohmura ◽  
Kazutaka Mukai ◽  
Yuji Takahashi ◽  
Toshiyuki Takahashi
Keyword(s):  
Skeletal Muscle ◽  
Tricarboxylic Acid Cycle ◽  
Maximal Oxygen Consumption ◽  
Incremental Exercise ◽  
Mass Spectrometry Analysis ◽  
Strenuous Exercise ◽  
Metabolomic Analysis ◽  
Exercise Tests ◽  
Spectrometry Analysis ◽  
Before And After

AbstractThoroughbreds have high maximal oxygen consumption and show hypoxemia and hypercapnia during intense exercise, suggesting that the peripheral environment in skeletal muscle may be severe. Changes in metabolites following extreme alterations in the muscle environment in horses after exercise may provide useful evidence. We compared the muscle metabolites before and after supramaximal exercise to fatigue in horses. Six well-trained horses ran until exhaustion in incremental exercise tests. Biopsy samples were obtained from the gluteus medius muscle before and immediately after exercise for capillary electrophoresis–mass spectrometry analysis. In the incremental exercise test, the total running time and speed of the last step were 10.4 ± 1.3 (mean ± standard deviation) min and 12.7 ± 0.5 m/s, respectively. Of 73 metabolites, 18 and 11 were significantly increased and decreased after exercise, respectively. The heat map of the hierarchical cluster analysis of muscle metabolites showed that changes in metabolites were clearly distinguishable before and after exercise. Strenuous exercise increased many metabolites in the glycolytic pathway and the tricarboxylic acid cycle in skeletal muscle. Targeted metabolomic analysis of skeletal muscle may clarify the intramuscular environment caused by exercise and explain the response of working muscles to strenuous exercise that induces hypoxemia and hypercapnia in Thoroughbred horses.

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