scholarly journals Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Taniya Roy Chowdhury ◽  
Joon-Yong Lee ◽  
Eric M. Bottos ◽  
Colin J. Brislawn ◽  
Richard Allen White ◽  
...  
Keyword(s):  
Climate Change ◽  
United States ◽  
Soil Moisture ◽  
Metabolic Pathways ◽  
Soil Microbial Communities ◽  
The United States ◽  
Soil Microbiome ◽  
Soil Drying ◽  
Soil Microbial ◽  
And Function

ABSTRACT Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community’s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies. IMPORTANCE Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycles carried out by soil microbiomes. In this study, we found that soil drying had a significant impact on the structure and function of soil microbial communities, including shifts in expression of specific metabolic pathways, such as those leading toward production of osmoprotectant compounds. This study demonstrates the application of an untargeted multi-omics approach to decipher details of the soil microbial community’s metaphenotypic response to environmental perturbations and should be applicable to studies of other complex microbial systems as well.

Assess 21st century Flash Drought in the United States using high resolution regional climate models

2021 ◽  
Author(s):  
Brandi Gamelin ◽  
Jiali Wang ◽  
V. Rao Kotamarthi
Keyword(s):  
Climate Change ◽  
United States ◽  
Soil Moisture ◽  
Climate Models ◽  
Wrf Model ◽  
The United States ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Regional Variability ◽  
Groundwater Levels

<p>Flash droughts are the rapid intensification of drought conditions generally associated with increased temperatures and decreased precipitation on short time scales.  Consequently, flash droughts are responsible for reduced soil moisture which contributes to diminished agricultural yields and lower groundwater levels. Drought management, especially flash drought in the United States is vital to address the human and economic impact of crop loss, diminished water resources and increased wildfire risk. In previous research, climate change scenarios show increased growing season (i.e. frost-free days) and drying in soil moisture over most of the United States by 2100. Understanding projected flash drought is important to assess regional variability, frequency and intensity of flash droughts under future climate change scenarios. Data for this work was produced with the Weather Research and Forecasting (WRF) model. Initial and boundary conditions for the model were supplied by CCSM4, GFDL-ESM2G, and HadGEM2-ES and based on the 8.5 Representative Concentration Pathway (RCP8.5). The WRF model was downscaled to a 12 km spatial resolution for three climate time frames: 1995-2004 (Historical), 2045-2054 (Mid), and 2085-2094 (Late).  A key characteristic of flash drought is the rapid onset and intensification of dry conditions. For this, we identify onset with vapor pressure deficit during each time frame. Known flash drought cases during the Historical run are identified and compared to flash droughts in the Mid and Late 21<sup>st</sup> century.</p>

scholarly journals Visualizing Microbial Community Dynamics via a Controllable Soil Environment

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Arunima Bhattacharjee ◽  
Dusan Velickovic ◽  
Thomas W. Wietsma ◽  
Sheryl L. Bell ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Soil Moisture ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
Soil Core ◽  
Soil Microbial ◽  
Functional Relationships ◽  
Microbial Community Dynamics

ABSTRACT Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.

scholarly journals SOILomics; where Microbiome Genetics meets Precision Agriculture

2021 ◽  
Vol 26 (1) ◽  
pp. e943
Author(s):  
Dimitrios Vlachakis ◽  
Aspasia Efthimiadou
Keyword(s):  
Climate Change ◽  
Precision Agriculture ◽  
Management Practices ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
New Techniques ◽  
New Era ◽  
Soil Microbial ◽  
Soil Biochemistry

Advances in genetics, soil biochemistry and microbiome analysis are opening up a new era in Precision Agriculture. In this direction, new techniques bring groundbreaking changes in land management practices through direct or indirect management of soil microbial communities. There is huge demand for the protection and enhancement of soil health and climate change resilience of crops. The increase in population, food consumption and fast approaching climate change pose a new threat to mankind that only by being proactive and highly prepared to deploy all novel and innovative stratagems in state-of-the-art soil microbiome precision agriculture can be avoided.

scholarly journals SOILomics; where Microbiome Genetics meets Precision Agriculture

2021 ◽  
Vol 26 ◽  
pp. e940
Author(s):  
Dimitrios Vlachakis ◽  
Aspasia Efthimiadou
Keyword(s):  
Climate Change ◽  
Precision Agriculture ◽  
Management Practices ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Soil Microbiome ◽  
New Techniques ◽  
New Era ◽  
Soil Microbial ◽  
Soil Biochemistry

Advances in genetics, soil biochemistry and microbiome analysis are opening up a new era in Precision Agriculture. In this direction, new techniques bring groundbreaking changes in land management practices through direct or indirect management of soil microbial communities. There is huge demand for the protection and enhancement of soil health and climate change resilience of crops. The increase in population, food consumption and fast approaching climate change pose a new threat to mankind that only by being proactive and highly prepared to deploy all novel and innovative stratagems in state-of-the-art soil microbiome precision agriculture can be avoided.

scholarly journals Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome

2021 ◽  
Author(s):  
Kishan Mahmud ◽  
Kendall Lee ◽  
Nicholas Hill ◽  
Ali Missaoui
Keyword(s):  
Tall Fescue ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
The United States ◽  
Fungal Endophyte ◽  
Plant Performance ◽  
Soil Microbiome ◽  
Grass Species ◽  
Rrna Gene ◽  
Soil Microbial

Abstract Background Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) is a popular perennial grass species for livestock production and amenities in the United States. Tall fescue often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala) which provides increased plant tolerance to environmental stress compared to endophyte-free plants. However, whether this improved plant performance is the sole result of the unique relationship between the grass and the shoot-dwelling fungal endophyte of rhizosphere origin remains a question. This symbiosis possibly regulates the recruitment of beneficial soil microbial communities in endophyte-infected tall fescue rhizosphere and may offer enhanced nutrients and water acquisition, thereby, providing the plant with an increased tolerance level against environmental stresses. We compared the soil bacterial and fungal community composition and investigated possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Results Our data revealed that bacterial community richness and the evenness indicated by Shannon Diversity Index (SDI) was greater than 4 in both endophyte-infected and endophyte-free tall fescue soil. In both types tall fescue soil, the prominent bacterial families were Planctomycetaceae, Balstocatellaceae_(subgroup_4), Chitinophagaceae, and Bacillaceae. In the case of soil fungal diversity, the SDI was overall low and ranged between 1.21 for endophyte-free and 1.27 for endophyte-infected tall fescue soil. The prominent fungal phyla were Basidiomycota and Ascomycota, and we observed a clear fungal community difference between endophyte-infected and endophyte-free soil at the phylum level. Moreover, endophyte-infected tall fescue soil showed a greater diversity at the genus level compared to endophyte-free tall fescue soil. In addition, plant-available soil phosphorus (P) is also influenced by the presence of endophytes in tall fescue. Conclusion Our results indicate that there is a tripartite relationship between tall fescue, the presence of fungal endophyte in the tall fescue, and the below-ground soil fungal communities. The dynamic of this three-way interaction perhaps contributes to the nutrient acquisition and stress tolerance by tall fescue possibly by recruiting a diverse array of potentially beneficial soil microbes.

scholarly journals Climate change mitigation as a co-benefit of regenerative ranching: insights from Australia and the United States

2020 ◽  
Vol 10 (5) ◽  
pp. 20200027 ◽  
Author(s):  
Hannah Gosnell ◽  
Susan Charnley ◽  
Paige Stanley
Keyword(s):  
Climate Change ◽  
United States ◽  
Climate Change Mitigation ◽  
Deep Understanding ◽  
The United States ◽  
Soil Microbiome ◽  
Ecological Processes ◽  
South Wales ◽  
The Right ◽  
Change Mitigation

‘Managed grazing’ is gaining attention for its potential to contribute to climate change mitigation by reducing bare ground and promoting perennialization, thereby enhancing soil carbon sequestration (SCS). Understanding why ranchers adopt managed grazing is key to developing the right incentives. In this paper, we explore principles and practices associated with the larger enterprise of ‘regenerative ranching’ (RR), which includes managed grazing but infuses the practice with holistic decision-making. We argue that this broader approach is appealing due to a suite of ecological, economic and social benefits, making climate change mitigation an afterthought, or ‘co-benefit’. RR is challenging, however, because it requires a deep understanding of ecological processes along with a set of skills related to monitoring and moving livestock and feeding the soil microbiome. We review the literature regarding links between RR and SCS, then present results of qualitative research focused on motivators, enablers and constraints associated with RR, drawing on interviews with 52 practitioners in New South Wales, Australia and the western United States. Our analysis is guided by a conceptual model of the social–ecological system associated with RR that identifies determinants of regenerative potential. We discuss implications for rancher engagement and conclude with a consideration of leverage points for global scalability.

scholarly journals Identification of Nonlinear Behavior in Transient Climate Change Projections of Soil Moisture over the United States

2009 ◽  
Vol 13 (1) ◽  
pp. 1-13
Author(s):  
Bruce T. Anderson ◽  
Catherine Reifen ◽  
Ralf Toumi
Keyword(s):  
Climate Change ◽  
United States ◽  
Soil Moisture ◽  
Nonlinear Behavior ◽  
The United States ◽  
Climate System ◽  
Future Climate Change ◽  
Climate Change Projections ◽  
Climate System Model

Abstract While most projections of climate change and its regional impacts focus on overall changes in the state of the climate system, useful information can also be found in the evolution of the climate system from one state to another. Here the authors introduce one method for identifying regions in which significant and systematic long-term nonlinear evolutions may be present, even given quasi-linear anthropogenic forcing. Using climate change projections taken from simulations of NCAR’s Community Climate System Model, version 3 (CCSM3), the authors then employ the technique to isolate systematic nonlinear behavior of soil moisture variations over the United States. While the projections presented here only represent the results from one model system, it is argued that such nonlinear behavior is an important characteristic of future climate change that should be considered when discussing both short-term and long-term impacts of anthropogenic climate forcing.

scholarly journals Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

GCB Bioenergy ◽  
2015 ◽  
Vol 8 (2) ◽  
pp. 481-494 ◽  
Author(s):  
Ederson da C. Jesus ◽  
Chao Liang ◽  
John F. Quensen ◽  
Endang Susilawati ◽  
Randall D. Jackson ◽  
...  
Keyword(s):  
United States ◽  
Microbial Communities ◽  
Cropping Systems ◽  
Soil Microbial Communities ◽  
The United States ◽  
Upper Midwest ◽  
Soil Microbial

scholarly journals An Attack on the Separation of Powers? Strategic Climate Litigation in the Eyes of U.S. Judges

2021 ◽  
Vol 13 (15) ◽  
pp. 8335
Author(s):  
Jasmina Nedevska
Keyword(s):  
Social Sciences ◽  
Climate Change ◽  
United States ◽  
Separation Of Powers ◽  
The United States ◽  
Checks And Balances ◽  
Climate Politics ◽  
The Social ◽  
Domestic Courts ◽  
Research Plan

Climate change litigation has emerged as a powerful tool as societies steer towards sustainable development. Although the litigation mainly takes place in domestic courts, the implications can be seen as global as specific climate rulings influence courts across national borders. However, while the phenomenon of judicialization is well-known in the social sciences, relatively few have studied issues of legitimacy that arise as climate politics move into courts. A comparatively large part of climate cases have appeared in the United States. This article presents a research plan for a study of judges’ opinions and dissents in the United States, regarding the justiciability of strategic climate cases. The purpose is to empirically study how judges navigate a perceived normative conflict—between the litigation and an overarching ideal of separation of powers—in a system marked by checks and balances.

Rethinking U.S. National Security after Covid19

2020 ◽  
Vol 26 (3) ◽  
Author(s):  
Linda J. Bilmes
Keyword(s):  
Climate Change ◽  
United States ◽  
National Security ◽  
The United States ◽  
Emerging Diseases ◽  
Defense Spending ◽  
Federal Spending ◽  
Us Economy ◽  
The Us ◽  
The Military

AbstractThe United States has traditionally defined national security in the context of military threats and addressed them through military spending. This article considers whether the United States will rethink this mindset following the disruption of the Covid19 pandemic, during which a non-military actor has inflicted widespread harm. The author argues that the US will not redefine national security explicitly due to the importance of the military in the US economy and the bipartisan trend toward growing the military budget since 2001. However, the pandemic has opened the floodgates with respect to federal spending. This shift will enable the next administration to allocate greater resources to non-military threats such as climate change and emerging diseases, even as it continues to increase defense spending to address traditionally defined military threats such as hypersonics and cyberterrorism.

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