scholarly journals Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 22 ◽  
Author(s):  
Daniel Rodríguez Amor ◽  
Martina Dal Bello
Keyword(s):  
Microbial Communities ◽  
Recent Progress ◽  
Population Level ◽  
Single Species ◽  
Major Question ◽  
Bottom Up ◽  
Microbial Ecosystems ◽  
Ecological Scales ◽  
Theoretical Predictions ◽  
The Stability

Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of these basic mechanisms, which were to some extent anticipated by theoretical predictions. Moreover, synthetic cooperation is a promising lead towards the engineering of novel functions and enhanced productivity of microbial communities. Here, we review recent progress on engineered cooperation in microbial ecosystems. We focus on bottom-up approaches that help to better understand cooperation at the population level, progressively addressing the challenges of tackling higher degrees of complexity: spatial structure, multispecies communities, and host-associated microbiomes. We envisage cooperation as a key ingredient in engineering complex microbial ecosystems.

scholarly journals Strength of species interactions determines biodiversity and stability in microbial communities

2019 ◽  
Author(s):  
Christoph Ratzke ◽  
Julien Barrere ◽  
Jeff Gore
Keyword(s):  
Microbial Communities ◽  
Species Interactions ◽  
Microbial Growth ◽  
Species Interaction ◽  
Nutrient Concentrations ◽  
History Of Research ◽  
Microbial Ecosystems ◽  
High Nutrient ◽  
History Of ◽  
The Stability

AbstractOrganisms – especially microbes – tend to live in complex communities. While some of these ecosystems are very bio-diverse, others aren’t1–3, and while some are very stable over time others undergo strong temporal fluctuations4,5. Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems6,7. Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems8–13, where an increase of ecosystem stability with biodiversity could be observed in several cases7,9,14. However, what causes these connections remains unclear. Here we show in microbial ecosystems in the lab that the concentrations of available nutrients can set the strength of interactions between bacteria. At high nutrient concentrations, extensive microbial growth leads to strong chemical modifications of the environment, causing more negative interactions between species. These stronger interactions exclude more species from the community – resulting in a loss of biodiversity. At the same time, these stronger interactions also decrease the stability of the microbial communities, providing a mechanistic link between species interaction, biodiversity and stability.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Polydomain Structure of Epitaxial PbTiO3 films on MgO

1997 ◽  
Vol 493 ◽  
Author(s):  
S. P. Alpay ◽  
A. S. Prakash ◽  
S. Aggarwal ◽  
R. Ramesh ◽  
A. L. Roytburd ◽  
...  
Keyword(s):  
Domain Structure ◽  
Pulsed Laser ◽  
Laser Deposition ◽  
X Ray Diffraction ◽  
X Ray ◽  
Theoretical Predictions ◽  
The Stability ◽  
Increasing Temperature ◽  
Stable Domains ◽  
Domain Stability

ABSTRACTA PbTiO3(001) film grown on MgO(001) by pulsed laser deposition is examined as an example to demonstrate the applications of the domain stability map for epitaxial perovskite films which shows regions of stable domains and fractions of domains in a polydomain structure. X-ray diffraction studies indicate that the film has a …c/a/c/a… domain structure in a temperature range of °C to 400°C with the fraction of c-domains decreasing with increasing temperature. These experimental results are in excellent agreement with theoretical predictions based on the stability map.

Interactions between steady and oscillatory convection in mushy layers

2010 ◽  
Vol 645 ◽  
pp. 411-434 ◽  
Author(s):  
PETER GUBA ◽  
M. GRAE WORSTER
Keyword(s):  
Standing Waves ◽  
Mushy Layer ◽  
Two Dimensional ◽  
Oscillatory Convection ◽  
Mushy Layers ◽  
Theoretical Predictions ◽  
Convection Patterns ◽  
The Stability ◽  
Nonlinear Solutions ◽  
Steady Convection

We study nonlinear, two-dimensional convection in a mushy layer during solidification of a binary mixture. We consider a particular limit in which the onset of oscillatory convection just precedes the onset of steady overturning convection, at a prescribed aspect ratio of convection patterns. This asymptotic limit allows us to determine nonlinear solutions analytically. The results provide a complete description of the stability of and transitions between steady and oscillatory convection as functions of the Rayleigh number and the compositional ratio. Of particular focus are the effects of the basic-state asymmetries and non-uniformity in the permeability of the mushy layer, which give rise to abrupt (hysteretic) transitions in the system. We find that the transition between travelling and standing waves, as well as that between standing waves and steady convection, can be hysteretic. The relevance of our theoretical predictions to recent experiments on directionally solidifying mushy layers is also discussed.

Stability of Water-Lubricated, Hydrostatic, Conical Bearings With Spiral Grooves for High-Speed Spindles

2001 ◽  
Vol 124 (2) ◽  
pp. 398-405 ◽  
Author(s):  
S. Yoshimoto ◽  
S. Oshima ◽  
S. Danbara ◽  
T. Shitara
Keyword(s):  
High Speed ◽  
Water Pressure ◽  
Rotating Shaft ◽  
Pressurized Water ◽  
High Speeds ◽  
Theoretical Predictions ◽  
The Stability ◽  
Stability Of Water ◽  
Spiral Grooves ◽  
Good Agreement

In this paper, the stability of water-lubricated, hydrostatic, conical bearings with spiral grooves for high-speed spindles is investigated theoretically and experimentally. In these bearing types, pressurized water is first fed to the inside of the rotating shaft and then introduced into spiral grooves through feeding holes located at one end of each spiral groove. Therefore, water pressure is increased due to the effect of the centrifugal force at the outlets of the feeding holes, which results from shaft rotation. In addition, water pressure is also increased by the viscous pumping effect of the spiral grooves. The stability of the proposed bearing is theoretically predicted using the perturbation method, and calculated results are compared with experimental results. It was consequently found that the proposed bearing is very stable at high speeds and theoretical predictions show good agreement with experimental data.

scholarly journals Predicting Collapse of Complex Ecological Systems: Quantifying the Stability-Complexity Continuum

2019 ◽  
Author(s):  
Susanne Pettersson ◽  
Van M. Savage ◽  
Martin Nilsson Jacobi
Keyword(s):  
Single Species ◽  
Ecological Systems ◽  
Ecological Research ◽  
Stability Criteria ◽  
Numerical Techniques ◽  
Intermediate Regime ◽  
Limits Of Stability ◽  
Species Abundances ◽  
The Stability ◽  
Degree Of Instability

Dynamical shifts between the extremes of stability and collapse are hallmarks of ecological systems. These shifts are limited by and change with biodiversity, complexity, and the topology and hierarchy of interactions. Most ecological research has focused on identifying conditions for a system to shift from stability to any degree of instability—species abundances do not return to exact same values after perturbation. Real ecosystems likely have a continuum of shifting between stability and collapse that depends on the specifics of how the interactions are structured, as well as the type and degree of disturbance due to environmental change. Here we map boundaries for the extremes of strict stability and collapse. In between these boundaries, we find an intermediate regime that consists of single-species extinctions, which we call the Extinction Continuum. We also develop a metric that locates the position of the system within the Extinction Continuum—thus quantifying proximity to stability or collapse—in terms of ecologically measurable quantities such as growth rates and interaction strengths. Furthermore, we provide analytical and numerical techniques for estimating our new metric. We show that our metric does an excellent job of capturing the system behaviour in comparison with other existing methods—such as May’s stability criteria or critical slowdown. Our metric should thus enable deeper insights about how to classify real systems in terms of their overall dynamics and their limits of stability and collapse.

scholarly journals Dynamic population stage structure due to juvenile–adult asymmetry stabilizes complex ecological communities

2021 ◽  
Vol 118 (21) ◽  
pp. e2023709118
Author(s):  
André M. de Roos
Keyword(s):  
Self Regulation ◽  
Interaction Network ◽  
Population Level ◽  
Stage Structure ◽  
Current Theory ◽  
Species Interaction ◽  
Interaction Matrix ◽  
Foraging Efficiency ◽  
Ecological Communities ◽  
The Stability

Natural ecological communities are diverse, complex, and often surprisingly stable, but the mechanisms underlying their stability remain a theoretical enigma. Interactions such as competition and predation presumably structure communities, yet theory predicts that complex communities are stable only when species growth rates are mostly limited by intraspecific self-regulation rather than by interactions with resources, competitors, and predators. Current theory, however, considers only the network topology of population-level interactions between species and ignores within-population differences, such as between juvenile and adult individuals. Here, using model simulations and analysis, I show that including commonly observed differences in vulnerability to predation and foraging efficiency between juvenile and adult individuals results in up to 10 times larger, more complex communities than observed in simulations without population stage structure. These diverse communities are stable or fluctuate with limited amplitude, although in the model only a single basal species is self-regulated, and the population-level interaction network is highly connected. Analysis of the species interaction matrix predicts the simulated communities to be unstable but for the interaction with the population-structure subsystem, which completely cancels out these instabilities through dynamic changes in population stage structure. Common differences between juveniles and adults and fluctuations in their relative abundance may hence have a decisive influence on the stability of complex natural communities and their vulnerability when environmental conditions change. To explain community persistence, it may not be sufficient to consider only the network of interactions between the constituting species.

Annular Liquid Jet Experiments

1980 ◽  
Vol 102 (3) ◽  
pp. 344-349 ◽  
Author(s):  
M. A. Hoffman ◽  
R. K. Takahashi ◽  
R. D. Monson
Keyword(s):  
Dimensionless Parameter ◽  
Maximum Velocity ◽  
Reliable Data ◽  
Liquid Jet ◽  
External Disturbances ◽  
Annular Jet ◽  
Theoretical Predictions ◽  
Series Of Experiments ◽  
The Stability ◽  
Surface Tension Forces

Experiments have been performed to determine the length for convergence or closure of a vertical, hollow annular water jet due to the action of surface tension forces. The data agree well with theoretical predictions up to the maximum velocity where reliable data could be obtained (4.4 m/s). These experiments extend the range of confirmation of the theories in terms of the dimensionless parameter, Nc ≡ We/Fr2, from about 0.01 to over 100. The stability of the annular jet subjected to natural and external disturbances is also discussed briefly. Finally the results of a series of experiments on the flow spreading or splitting due to the presence of wedge-shaped obstacles in the path of the annular jet flow are presented.

scholarly journals Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

2013 ◽  
Vol 16 (6) ◽  
pp. 1472-1481 ◽  
Author(s):  
Karen De Roy ◽  
Massimo Marzorati ◽  
Pieter Van den Abbeele ◽  
Tom Van de Wiele ◽  
Nico Boon
Keyword(s):  
Microbial Communities ◽  
Microbial Ecosystems

scholarly journals Synthesis of distorted nanographenes containing seven- and eight-membered carbocycles

2018 ◽  
Vol 54 (50) ◽  
pp. 6705-6718 ◽  
Author(s):  
Irene R. Márquez ◽  
Silvia Castro-Fernández ◽  
Alba Millán ◽  
Araceli G. Campaña
Keyword(s):  
Recent Progress ◽  
Polyaromatic Hydrocarbons ◽  
Bottom Up

We highlight recent progress in bottom-up synthesis of well-defined distorted polyaromatic hydrocarbons with saddle shapes containing heptagonal and octagonal carbocycles.

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