Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

Meng, Dong; Yang, Zhijian; Cheng, Guangyuan; Lei, Peng; Xu, Qian; Xu, Jianhong

doi:10.3389/fmicb.2018.00267

Cited by 56 publications

(37 citation statements)

References 58 publications

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“…Nitrogen fertilization of switchgrass reduces the ability of the soil microbiome to evolve into a diverse community that resembles that under long-term prairies (Oates et al, 2016). Host-microbe associations are heritable (Peiffer et al, 2013), and this variation can be used to identify and select genotypes with superior abilities to benefit from these associations from an agronomic viewpoint (Lima et al, 1987;Urquiaga et al, 1992;Dong et al, 2018). There is some evidence for genetic or ecotypic variability in host-microbe nutrient dynamics within switchgrass, supporting a hypothesis that high-biomass cultivars will be better able to support a bacterial community with high nitrogenase activity compared with low-biomass cultivars (Rodrigues et al, 2017).…”

Section: Nitrogen: To Fertilize or Notmentioning

confidence: 99%

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

et al. 2019

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Development of switchgrass (Panicum virgatum L.) as a dedicated bioenergy feedstock requires intensive and extensive breeding programs that include careful and thoughtful consideration of appropriate target populations of environments (TPEs). The purpose of this study was to evaluate region (climate), soil quality, and N fertilization level as potential factors influencing the choice of TPE. A total of 45 switchgrass genotypes were evaluated in uniform field studies at six field sites defined as prime or marginal soils in New Jersey, South Dakota, and Wisconsin. Region and soil quality had strong interactions with genotype, but N fertilization had little impact on genetic variation or ranking of genotypes. Lowland genotypes were considerably more sensitive than upland genotypes to interactions with environmental factors, probably due to these field sites being outside of the traditional lowland adaptation zones. Genotype rankings were highly inconsistent across regions and soil types, indicating that breeding programs that target marginal soils should be located on soils that represent the appropriate TPE. Furthermore, interactions across the three regions suggest that breeding programs for the lowland ecotype should be subdivided into different sets of TPEs, which are largely a function of hardiness zone and annual precipitation. Lastly, even with negligible interactions involving N fertilization level, future definitions of TPEs should be based on minimal or no N fertilizer applications to allow breeders to select plants with greater N‐use efficiency, N‐scavenging ability, and N‐recycling efficiency.

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Section: Nitrogen: To Fertilize or Notmentioning

confidence: 99%

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

et al. 2019

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“…First, temporal oscillations are an essential physical phenomena in living systems. Examples include the cell cycle [11], bacterial circadian rhythms [12][13][14] and other biochemical oscillations [15,16]. Genetic oscillators have also been designed in synthetic biology [17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Subharmonic oscillations in stochastic systems under periodic driving

2019

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Subharmonic response is a well known phenomena in, e.g., deterministic nonlinear dynamical systems. We investigate the conditions under which such subharmonic oscillations can persist for a long time in open systems with stochastic dynamics due to thermal fluctuations. In contrast to stochastic autonomous systems in a stationary state, for which the number of coherent oscillations is fundamentally bounded by the number of states in the underlying network, we demonstrate that in periodically driven systems, subharmonic oscillations can, in principle, remain coherent forever, even in networks with a small number of states. We also show that, inter alia, the thermodynamic cost rises only logarithmically with the number of coherent oscillations in a model calculation and that the possible periods of the persistent subharmonic response grow linearly with the number of states. We argue that our results can be relevant for biochemical oscillations and for stochastic models of time-crystals.

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“…They often take place in autonomous nonequilibrium noisy systems that dissipate energy to sustain the oscillations. Prominent examples are autonomous biochemical oscillators, such as systems of interacting molecules that display circadian rhythms driven by the consumption of chemical energy [1,2].…”

Section: Introductionmentioning

confidence: 99%

Oscillations in feedback-driven systems: Thermodynamics and noise

Martino

Barato

2019

Phys. Rev. E

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Oscillations in nonequilibrium noisy systems are important physical phenomena. These oscillations can happen in autonomous biochemical oscillators such as circadian clocks. They can also manifest as subharmonic oscillations in periodically driven systems such as time-crystals. Oscillations in autonomous systems and, to a lesser degree, subharmonic oscillations in periodically driven systems have been both thoroughly investigated, including their relation with thermodynamic cost and noise. We perform a systematic study of oscillations in a third class of nonequilibrium systems: feedback driven systems. In particular, we use the apparatus of stochastic thermodynamics to investigate the role of noise and thermodynamic cost in feedback driven oscillations. For a simple two-state model that displays oscillations, we analyze the relation between precision and dissipation, revealing that oscillations can remain coherent for an indefinite time in a finite system with thermal fluctuations in a limit of diverging thermodynamic cost. We consider oscillations in a more complex system with several degrees of freedom, an Ising model driven by feedback between the magnetization and the external field. This feedback driven system can display subharmonic oscillations similar to the ones observed in time-crystals. We illustrate the second law for feedback driven systems that display oscillations. For the Ising model, the oscillating dissipated heat can be negative. However, when we consider the total entropy that also includes an informational term related to measurements, the oscillating total entropy change is always positive. We also study the finite-size scaling of the dissipated heat, providing evidence for the existence of a first-order phase transition for certain parameter regimes.

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Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum

Cited by 56 publications

References 58 publications

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

Soil Quality and Region Influence Performance and Ranking of Switchgrass Genotypes

Subharmonic oscillations in stochastic systems under periodic driving

Oscillations in feedback-driven systems: Thermodynamics and noise

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