Soil microbial systems respond differentially to tetracycline, sulfamonomethoxine, and ciprofloxacin entering soil under pot experimental conditions alone and in combination

2014 ◽  
Vol 21 (12) ◽  
pp. 7436-7448 ◽  
Author(s):  
Junwei Ma ◽  
Hui Lin ◽  
Wanchun Sun ◽  
Qiang Wang ◽  
Qiaogang Yu ◽  
...  
Keyword(s):  
Experimental Conditions ◽  
Soil Microbial ◽  
Microbial Systems

scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Vol 116 (51) ◽  
pp. 25900-25908 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Marker Genes ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Root Litter ◽  
Viral Communities ◽  
Microbial Systems

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity wasNarnaviridaethat may parasitize fungi orLeviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics byLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

scholarly journals Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Grace Pold ◽  
Luiz A. Domeignoz-Horta ◽  
Kristen M. DeAngelis
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Growth ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Growth Efficiency ◽  
Experimental Conditions ◽  
Soil Microbial ◽  
Use Efficiency ◽  
Microbial Growth Efficiency

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

scholarly journals Animal soil food web complexity triggers shifts in microbial communities, including PAH degraders, but without clear effects on phenanthrene phytoremediation

2021 ◽  
Author(s):  
Sara Correa-García ◽  
Vincenzo Corelli ◽  
Julien Tremblay ◽  
Jessica Ann Dozois ◽  
Eugenie Mukula ◽  
...  
Keyword(s):  
Food Web ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Soil Food Web ◽  
Experimental Conditions ◽  
Bacterial Phyla ◽  
Soil Microbial ◽  
Degradation Rates ◽  
Food Web Complexity

The aim of this study was to determine whether the complexity of the animal soil food web (SFWC) is a significant factor influencing the soil microbial communities, the productivity of the willow, and the degradation rates of 100 mg kg-1 phenanthrene contamination. The SFWC treatment had eight levels: just the microbial community (BF), or the BF with nematodes (N), springtails (C), earthworms (E), CE, CN, EN, CEN. After eight weeks of growth, the height and biomass of willows were significantly affected by the SFWC, whereas the amount of phenanthrene degraded was not affected, reaching over 95% in all pots. SFWC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFWC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many PAH degraders. These SFWC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to the Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFWC treatments. Overall, our results suggest that, under our experimental conditions, SFWC does not affect significantly willow phytoremediation outcomes.

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

2021 ◽  
Author(s):  
Arthur Escalas ◽  
Fabiana S. Paula ◽  
François Guilhaumon ◽  
Mengting Yuan ◽  
Yunfeng Yang ◽  
...  
Keyword(s):  
Functional Organization ◽  
Gene Variants ◽  
Soil Microbial ◽  
Microbial Systems

scholarly journals Microcosm Experiment to Assess the Capacity of a Poplar Clone to Grow in a PCB-Contaminated Soil

Water ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2220 ◽  
Author(s):  
Isabel Nogues ◽  
Paola Grenni ◽  
Martina Di Lenola ◽  
Laura Passatore ◽  
Ettore Guerriero ◽  
...  
Keyword(s):  
Microbial Community ◽  
Contaminated Soil ◽  
Hybrid Poplar ◽  
Hypoxic Condition ◽  
Soil Conditions ◽  
Natural Soil ◽  
Experimental Conditions ◽  
Soil Microbial ◽  
Poplar Clone ◽  
Set Up

Polychlorinated byphenyls (PCBs) are a class of Persistent Organic Pollutants extremely hard to remove from soil. The use of plants to promote the degradation of PCBs, thanks to synergic interactions between roots and the natural soil microorganisms in the rhizosphere, has been proved to constitute an effective and environmentally friendly remediation technique. Preliminary microcosm experiments were conducted in a greenhouse for 12 months to evaluate the capacity of the Monviso hybrid poplar clone, a model plant for phytoremediation, to grow in a low quality and PCB-contaminated soil in order to assess if this clone could be subsequently used in a field experiment. For this purpose, three different soil conditions (Microbiologically Active, Pre-sterilized and Hypoxic soils) were set up in order to assess the capacity of this clone to grow in the polluted soil in these different conditions and support the soil microbial community activity. The growth and physiology (chlorophyll content, chlorophyll fluorescence, ascorbate, phenolic compounds and flavonoid contents) of the poplar were determined. Moreover, chemical analyses were performed to assess the concentrations of PCB indicators in soil and plant roots. Finally, the microbial community was evaluated in terms of total abundance and activity under the different experimental conditions. Results showed that the poplar clone was able to grow efficiently in the contaminated soil and to promote microbial transformations of PCBs. Plants grown in the hypoxic condition promoted the formation of a higher number of higher-chlorinated PCBs and accumulated lower PCBs in their roots. However, plants in this condition showed a higher stress level than the other microcosms, producing higher amounts of phenolic, flavonoid and ascorbate contents, as a defence mechanism.

scholarly journals Reducing N Fertilization without Yield Penalties in Maize with a Commercially Available Seed Dressing

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 407 ◽  
Author(s):  
Stefania Codruta Maris ◽  
Federico Capra ◽  
Federico Ardenti ◽  
Marcello E. Chiodini ◽  
Roberta Boselli ◽  
...  
Keyword(s):  
Grain Yield ◽  
Root Length Density ◽  
Maize Yield ◽  
N Fertilization ◽  
N2o Emissions ◽  
Experimental Conditions ◽  
N Losses ◽  
Soil Microbial ◽  
Seed Dressing ◽  
Productivity Potential

Introducing smart and sustainable tools for climate change adaptation and mitigation is a major need to support agriculture’s productivity potential. We assessed the effects of the processed gypsum seed dressing SOP® COCUS MAIZE+ (SCM), combined with a gradient of N fertilization rates (i.e., 0%, 70% equal to 160 kg N ha−1, and 100% equal to 230 kg N ha−1) in maize (Zea mays L.), on: (i) grain yield, (ii) root length density (RLD) and diameter class length (DCL), (iii) biodiversity of soil bacteria and fungi, and (iv) Greenhouse Gases (GHGs, i.e., N2O, CO2, and CH4) emission. Grain yield increased with SCM by 1 Mg ha−1 (+8%). The same occurred for overall RLD (+12%) and DCL of very fine, fine, and medium root classes. At anthesis, soil microbial biodiversity was not affected by treatments, suggesting earlier plant-rhizosphere interactions. Soil GHGs showed that (i) the main driver of N losses as N2O is the N-fertilization level, and (ii) decreasing N-fertilization in maize from 100% to 70% decreased N2O emissions by 509 mg N-N2O m−2 y−1. Since maize grain yield under SCM with 70% N-fertilization was similar to that under Control with 100% N-fertilization, we concluded that under our experimental conditions SCM may be used for reducing N input (−30%) and N2O emissions (−23%), while contemporarily maintaining maize yield. Hence, SCM can be considered an available tool to improve agriculture’s alignment to the United Nation Sustainable Development Goals (UN SDGs) and to comply with Europe’s Farm to Fork strategy for reducing N-fertilizer inputs.

Significance of phenolic compounds in plant‐soil‐microbial systems

1991 ◽  
Vol 10 (1) ◽  
pp. 63-121 ◽  
Author(s):  
José O. Siqueira ◽  
Muraleedharan G. Nair ◽  
Raymond Hammerschmidt ◽  
Gene R. Safir ◽  
Alan R. Putnam
Keyword(s):  
Phenolic Compounds ◽  
Soil Microbial ◽  
Plant Soil ◽  
Microbial Systems

Electrolytic Isolation of Twin-Type Shock Deformation Structures

1967 ◽  
Vol 25 ◽  
pp. 318-319
Author(s):  
F. I. Grace ◽  
L. E. Murr
Keyword(s):  
Grain Boundaries ◽  
Thin Foil ◽  
Electrolyte Composition ◽  
Experimental Conditions ◽  
Average Current Density ◽  
Electron Transmission ◽  
Deformation Structures ◽  
The Matrix ◽  
Average Current ◽  
Specimen Edge

During the course of electron transmission investigations of the deformation structures associated with shock-loaded thin foil specimens of 70/30 brass, it was observed that in a number of instances preferential etching occurred along grain boundaries; and that the degree of etching appeared to depend upon the various experimental conditions prevailing during electropolishing. These included the electrolyte composition, the average current density, and the temperature in the vicinity of the specimen. In the specific case of 70/30 brass shock-loaded at pressures in the range 200-400 kilobars, the predominant mode of deformation was observed to be twin-type faults which in several cases exhibited preferential etching similar to that observed along grain boundaries. A novel feature of this particular phenomenon was that in certain cases, especially for twins located in the vicinity of the specimen edge, the etching or preferential electropolishing literally isolated these structures from the matrix.

Site of Lysosome Production During Hepatic Injury

1969 ◽  
Vol 27 ◽  
pp. 348-349
Author(s):  
Nalin J. Unakar
Keyword(s):  
Electron Microscopy ◽  
Golgi Apparatus ◽  
Mouse Liver ◽  
Hepatic Injury ◽  
Close Approximation ◽  
Experimental Conditions ◽  
Toxic Injury

The increased number of lysosomes as well as the close approximation of lysosomes to the Golgi apparatus in tissue under variety of experimental conditions is commonly observed. These observations suggest Golgi involvement in lysosomal production. The role of the Golgi apparatus in the production of lysosomes in mouse liver was studied by electron microscopy of liver following toxic injury by CCI4.

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