scholarly journals Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bridget B. McGivern ◽  
Malak M. Tfaily ◽  
Mikayla A. Borton ◽  
Suzanne M. Kosina ◽  
Rebecca A. Daly ◽  
...  
Keyword(s):  
Organic Matter ◽  
Nutrient Cycling ◽  
Microbial Degradation ◽  
Soil Type ◽  
Degradation Products ◽  
Soil Microbiome ◽  
Wetland Soil ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Soil Ecosystems

AbstractMicroorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

scholarly journals Investigating the drought-prone biological interplay of soil microbial communities and Scots pine trees 

2021 ◽  
Author(s):  
Astrid Jäger ◽  
Martin Hartmann ◽  
Frank Hagedorn ◽  
Johan Six ◽  
Emily Solly
Keyword(s):  
Nutrient Cycling ◽  
Microbial Communities ◽  
Scots Pine ◽  
Tree Mortality ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Tree Vitality ◽  
Soil Microbial ◽  
Pine Trees ◽  
Effects Of Drought

<p>In forest ecosystems, microorganisms hold key functions as nutrient cyclers, decomposers, plant symbionts or pathogens and thereby regulate biogeochemical processes and forest health. These microbial dynamics are controlled by water availability in three fundamental ways: as resource, as solvent, and as transport medium. For one of the dominant tree species in Swiss forests - Scots pine (Pinus sylvestris L.) - high mortality rates have been observed in recent decades. In the Rhone valley of Switzerland, forest dieback appears to be primarily caused by direct effects of drought and an increasing susceptibility of trees to further constraints, such as pathogen attacks. Nonetheless, water limitation does not affect soil microbes and trees separately but rather induces a series of interconnected effects between trees and the associated soil microbiome, which could strongly alter carbon and nutrient cycling in forests. We conduct a study to investigate the effects of drought on the biological interplay between Scots pine trees and soil microbial communities. We aim to estimate how shifts in microbial community composition and functional capacity under drought may affect nutrient cycling and tree vitality potentially contributing to tree mortality. In order to understand these mechanisms, we perform greenhouse experiments with tree-soil mesocosms under controlled conditions. State-of-the art molecular methods such as metabarcoding of ribosomal markers, shotgun metagenome sequencing, and qPCR of key functional genes are used to unravel alterations in the soil microbiome and in the underlying functional metabolic potential related to drought and associated tree-mortality. Furthermore, to elucidate the impact of drought on microbial carbon dynamics, stable isotope labelling techniques have been applied to trace <sup>13</sup>C labeled plant photosynthates into the soil microbial communities by analyzing <sup>13</sup>C signatures of phospholipid fatty acids. Investigation of soil physicochemical properties and tree-vitality is done in parallel with the microbial assessments to understand the feedbacks on nutrient-cycling and the soil-tree continuum. The overarching aim of this study is to gain new insights into the complex relationships between soil, trees and microbes under drought.</p>

scholarly journals THE SOIL MICROBIAL COENOSIS STATE UNDER VARIOUS CROPS IN CASE OF INTRODUCING THE MIXTURE OF SILICON-CONTAINING MINERALS

2015 ◽  
Vol 22 ◽  
pp. 30-36
Author(s):  
N. E. Ellanska ◽  
N. V. Zaimenko ◽  
O. P. Yunosheva
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Sugar Beet ◽  
Soil Microbial Communities ◽  
Trophic Groups ◽  
Rhizospheric Soil ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Corn Plants ◽  
Positive Effect

In the conditions of stationary experiment the features of the formation of microbial coenosis in the rhizosphere of sugar beet, soybean and corn plants were studied in case of introducing silicon-containing mixtures into the soil. It was shown that the number of representatives of separate eco-trophic groups of microorganisms varies depending on the culture and introduced mixture. Soil microbial communities from under soybean and corn were characterized by the biggest changes, especially in case of mineralized sapropel introduction. Positive effect on sugar beet rhizospheric soil microbiota was made by mixtures: high-bog peat + siliconcontaining minerals and potassium silicate + silicon-containing minerals + sapropel. The processes of soil organic matter mineralization were quite balanced.

Adsorption, Mobility, and Microbial Degradation of Glyphosate in the Soil

Weed Science ◽  
1975 ◽  
Vol 23 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Paul Sprankle ◽  
W. F. Meggitt ◽  
Donald Penner
Keyword(s):  
Organic Matter ◽  
Microbial Degradation ◽  
Phosphonic Acid ◽  
Soil Type ◽  
Ethyl Cellulose ◽  
Bentonite Clay ◽  
Acid Moiety ◽  
Pka Values ◽  
Potentiometric Titrations ◽  
Adsorption Sites

Glyphosate [N-(phosphonomethyl)glycine] was readily bound to kaolinite, illite, and bentonite clay and to charcoal and muck but not to ethyl cellulose. Fe+++ and Al+++-saturated clays and organic matter adsorbed more glyphosate than Na+ or Ca+-saturated clays and organic matter. Glyphosate appears to be bound to the soil through the phosphonic acid moiety as phosphate in the soil competed with 14C-glyphosate for adsorption sites. Glyphosate mobility in the soil was very limited and was affected by pH, phosphate level, and soil type. The 14C-glyphosate was biodegraded in soil to 14CO2 possibly by co-metabolism. Potentiometric titrations of the compound gave pKa values of 2, 2.6, 5.6, and 10.6.

scholarly journals Genetic and Metabolic Diversity of Soil Microbiome in Response to Exogenous Organic Matter Amendments

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 546 ◽  
Author(s):  
Agata Gryta ◽  
Magdalena Frąc ◽  
Karolina Oszust
Keyword(s):  
Organic Matter ◽  
Microbial Diversity ◽  
Organic Waste ◽  
Organic Matter Content ◽  
Matter Content ◽  
Soil Microbiome ◽  
Soil Microbial ◽  
Essential Components ◽  
Microbiological Parameters ◽  
Dehydrogenases Activity

Loss of organic matter content of cultivated soils is observed in many regions of Europe. The possibility of using organic waste as a soil additive that enriches the soil with organic matter and essential components is important in soil quality protection and waste management. This research concerned the influence of six organic wastes—two industrial composts, three digestates and meat bone meal—on soil microbial properties. The study of functional microbial diversity concerns the determination of the catabolic capacity of bacterial, fungal and anaerobic communities in relation to carbon substrates in metabolic profiling plates (Biolog® ECO, FF, AN (Biolog Inc., Hayward, CA, USA)). The assessment of genetic diversity was made on the basis of analysis of the restriction profile of ammonia-oxidizing archaea. Additionally, soil dehydrogenases activity was determined. The research showed that the type of organic waste used had an influence on the microbiological parameters. The application of exogenous organic matter caused increases in functional and genetic microbial diversity. The nature of the noted changes was short term and periodic. The values of the microbiological parameters in soils with organic waste were similar to those of the control samples. This indicates an improved microbiological balance and stability of the soil environment after the application of exogenous organic matter.

Role of microbial reducing activity in antimony and arsenic release from an unpolluted wetland soil: a lab scale study using sodium azide as a microbial inhibiting agent

2016 ◽  
Vol 13 (6) ◽  
pp. 945 ◽  
Author(s):  
Asmaa Rouwane ◽  
Marion Rabiet ◽  
Isabelle Bourven ◽  
Malgorzata Grybos ◽  
Lucie Mallet ◽  
...  
Keyword(s):  
Organic Matter ◽  
Sodium Azide ◽  
Apparent Molecular Weight ◽  
Wetland Soil ◽  
Soil Microbial ◽  
Reducing Conditions ◽  
Key Factor ◽  
Reducing Activity ◽  
The Given

Environmental contextAntimony and arsenic are toxic elements occurring naturally in the environment. We found that arsenic release to water from an unpolluted wetland soil is related to microbial reducing activity only, whereas antimony can still be released when this activity is inhibited, suggesting the involvement of additional processes. The findings show that microbial/non-microbial mechanisms control arsenic and antimony release and can thereby impact water quality at wetland outlets. AbstractIn wetland soils, the mobility of geogenic metal(loid)s is usually associated with direct or indirect microbial-induced processes (solubilisation of mineral and organic components, pH induced desorption, competition effects, dissimilatory reduction). To identify the role of microbial reducing activity in As and Sb release, we conducted two series of soil incubations (sodium azide-treated (NaN3-T) and non-treated (NT)) in closed batches for 36 days. During the incubation period, we monitored the evolution of dissolved As, Sb, Mn, FeII, organic carbon (DOC), humic substances (HS) and proteins (PN) with their apparent molecular weight distribution (aMW) as well as pH, reduction potential (Eh) and alkalinity. Results showed that the release of As and Sb occurred when microbially reducing conditions prevailed (NT soil Eh ~0mV and FeII>40mg L–1) and was inhibited for As in the absence of microbial reducing activity (NaN3-T soil; Eh>250mV and Fe<1mg L–1). In contrast, Sb behaved differently since its release was only slowed down when microbially reducing conditions were inhibited. We concluded that soil microbial reducing activity fully controls the release of As and to a lesser extent that of Sb when NaN3 is used as a microbial inhibiting agent. Since Sb release and dissolved organic matter (DOM) solubilisation (NaN3-induced artefact) occurred simultaneously in the absence of microbially reducing conditions, we concluded that organic matter could be one key factor controlling Sb mobilisation in the given conditions, which is not the case for As.

scholarly journals Polar ice core organic matter signatures reveal past atmospheric carbon composition and spatial trends across ancient and modern timescales

2021 ◽  
pp. 1-15
Author(s):  
Juliana D'Andrilli ◽  
Joseph R. McConnell
Keyword(s):  
Organic Matter ◽  
Amino Acid ◽  
Microbial Degradation ◽  
Degradation Products ◽  
Ice Core ◽  
Ice Cores ◽  
Polar Ice ◽  
Higher Plant ◽  
Global Comparison ◽  
Spatiotemporal Scales

Abstract We present polar ice core organic matter (OM) fluorescence signatures to reconstruct ancient and modern atmospheric compositions and relate OM signals to past ecological changes. OM composition from three Arctic ice cores (Canada and Greenland) was characterized by fluorescence spectroscopy and compared to an Antarctic OM record. Diverse OM was measured in ancient and modern ice in both hemispheres and similarities existed across vast spatiotemporal scales. We determined three OM markers, indicating paleoclimate and modern carbon trends: (i) ‘humic-like’, detected in Holocene ice of more complex and aromatic character, supporting trends of higher plant influences in warmer climates, (ii) monolignol- and non-amino acid-like, describing simple, lignin-like OM precursors ubiquitous in the environment and the microbial degradation products of more complex materials from plants/soils, and (iii) amino acid- and tannin-like, indicating microbial degradation of simple OM chemical species, compared to the other markers. Concentration trends were inferred from fluorescence intensities of individual OM types and related to warmer temperatures. No indicators of freshly produced OM by microbes were detected; signals were interpreted as materials externally produced from the ice and transported to polar regions. This marks the first global comparison of atmospheric reconstructions from OM across vast spatiotemporal scales.

scholarly journals A Quantitative Analysis of Factors Influencing Organic Matter Concentration in the Topsoil of Black Soil in Northeast China Based on Spatial Heterogeneous Patterns

2021 ◽  
Vol 10 (5) ◽  
pp. 348
Author(s):  
Zhenbo Du ◽  
Bingbo Gao ◽  
Cong Ou ◽  
Zhenrong Du ◽  
Jianyu Yang ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Soil Erosion ◽  
Soil Type ◽  
Northeast China ◽  
Black Soil ◽  
Factors Affecting ◽  
Soil Zone ◽  
Rainfed Farming ◽  
Study Results

Black soil is fertile, abundant with organic matter (OM) and is exceptional for farming. The black soil zone in northeast China is the third-largest black soil zone globally and produces a quarter of China’s commodity grain. However, the soil organic matter (SOM) in this zone is declining, and the quality of cultivated land is falling off rapidly due to overexploitation and unsustainable management practices. To help develop an integrated protection strategy for black soil, this study aimed to identify the primary factors contributing to SOM degradation. The geographic detector, which can detect both linear and nonlinear relationships and the interactions based on spatial heterogeneous patterns, was used to quantitatively analyze the natural and anthropogenic factors affecting SOM concentration in northeast China. In descending order, the nine factors affecting SOM are temperature, gross domestic product (GDP), elevation, population, soil type, precipitation, soil erosion, land use, and geomorphology. The influence of all factors is significant, and the interaction of any two factors enhances their impact. The SOM concentration decreases with increased temperature, population, soil erosion, elevation and terrain undulation. SOM rises with increased precipitation, initially decreases with increasing GDP but then increases, and varies by soil type and land use. Conclusions about detailed impacts are presented in this paper. For example, wind erosion has a more significant effect than water erosion, and irrigated land has a lower SOM content than dry land. Based on the study results, protection measures, including conservation tillage, farmland shelterbelts, cross-slope ridges, terraces, and rainfed farming are recommended. The conversion of high-quality farmland to non-farm uses should be prohibited.

scholarly journals Effect of Plant Growth Regulators on Protease Activity in Forest Floor of Norway Spruce Stand

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 665
Author(s):  
Ladislav Holik ◽  
Jiří Volánek ◽  
Valerie Vranová
Keyword(s):  
Organic Matter ◽  
Proteolytic Activity ◽  
Protease Activity ◽  
Forest Floor ◽  
Soil Microbial Activity ◽  
Inhibitory Effects ◽  
Chlorocholine Chloride ◽  
Soil Microbial ◽  
Native Soil ◽  
Transformation Processes

Soil proteases are involved in organic matter transformation processes and, thus, influence ecosystem nutrient turnovers. Phytohormones, similarly to proteases, are synthesized and secreted into soil by fungi and microorganisms, and regulate plant rhizosphere activity. The aim of this study was to determine the effect of auxins, cytokinins, ethephon, and chlorocholine chloride on spruce forest floor protease activity. It was concluded that the presence of auxins stimulated native proteolytic activity, specifically synthetic auxin 2-naphthoxyacetic acid (16% increase at added quantity of 5 μg) and naturally occurring indole-3-acetic acid (18%, 5 μg). On the contrary, cytokinins, ethephon and chlorocholine chloride inhibited native soil protease activity, where ethephon (36% decrease at 50 μg) and chlorocholine chloride (34%, 100 μg) showed the highest inhibitory effects. It was concluded that negative phytohormonal effects on native proteolytic activity may slow down organic matter decomposition rates and hence complicate plant nutrition. The study enhances the understanding of rhizosphere exudate effects on soil microbial activity and soil nitrogen cycle.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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