scholarly journals Allopatric divergence limits cheating range and alters genetic requirements for a cooperative trait

2021 ◽  
Author(s):  
Kaitlin A Schaal ◽  
Yuen-Tsu Nicco Yu ◽  
Marie Vasse ◽  
Gregory J Velicer
Keyword(s):  
Genomic Context ◽  
Geographic Mosaic ◽  
Multicellular Development ◽  
Cooperative Development ◽  
Developmental System Drift ◽  
Wide Range ◽  
Allopatric Divergence ◽  
Natural Isolates ◽  
Microbial System ◽  
Mixed Groups

Social and genomic context may constrain the fates of mutations in cooperation genes. While some mechanisms limiting cheaters evolve in the presence of cheating, here we ask whether cheater resistance can evolve latently even in environments where cooperation is not expressed and cheaters are absent. The bacterium Myxococcus xanthus undergoes cooperative multicellular development upon starvation, but developmentally defective cheaters can outcompete cooperators within mixed groups. Using natural isolates and an obligate cheater disrupted at the developmental-signaling gene csgA, we show that cheating range is narrow among natural strains due to antagonisms that do not specifically target cheaters. Further, we mixed the cheater with closely related cooperators that diverged from it allopatrically in nutrient-rich environments in which cooperative development does not occur, showing that even slight divergence under these conditions can eliminate cheating phenotypes. Our results suggest that such cooperation- and cheater-blind divergence can generate a geographic mosaic of local cheater-cooperator compatibility patches that limit cheater spread. We also ask whether genomic divergence can shape the fitness effects of disrupting a cooperation gene. Construction of the same csgA mutation in several natural-isolate cooperators generated a wide range of pure-culture sporulation phenotypes, from a complete defect to no defect. Thus, we find that epistatic interactions limit the range of genomes within which a mutation creates a cooperation defect. Moreover, these results reveal Developmental System Drift in a microbial system because sporulation proficiency is conserved across the natural isolates despite divergence in the role of csgA.

scholarly journals Social complementation and growth advantages promote socially defective bacterial isolates

2014 ◽  
Vol 281 (1781) ◽  
pp. 20140036 ◽  
Author(s):  
Susanne A. Kraemer ◽  
Gregory J. Velicer
Keyword(s):  
Social Interactions ◽  
Fruiting Body ◽  
Natural Populations ◽  
Developmental Defects ◽  
Multicellular Development ◽  
Evolutionary Forces ◽  
Natural Isolates ◽  
Multiple Cycles ◽  
Low Levels ◽  
Mixed Groups

Social interactions among diverse individuals that encounter one another in nature have often been studied among animals but rarely among microbes. For example, the evolutionary forces that determine natural frequencies of bacteria that express cooperative behaviours at low levels remain poorly understood. Natural isolates of the soil bacterium Myxococcus xanthus sampled from the same fruiting body often vary in social phenotypes, such as group swarming and multicellular development. Here, we tested whether genotypes highly proficient at swarming or development might promote the persistence of less socially proficient genotypes from the same fruiting body. Fast-swarming strains complemented slower isolates, allowing the latter to keep pace with faster strains in mixed groups. During development, one low-sporulating strain was antagonized by high sporulators, whereas others with severe developmental defects had those defects partially complemented by high-sporulating strains. Despite declining in frequency overall during competition experiments spanning multiple cycles of development, developmentally defective strains exhibited advantages during the growth phases of competitions. These results suggest that microbes with low-sociality phenotypes often benefit from interacting with more socially proficient strains. Such complementation may combine with advantages at other traits to increase equilibrium frequencies of low-sociality genotypes in natural populations.

Barcoded microbial system for high-resolution object provenance

Science ◽  
2020 ◽  
Vol 368 (6495) ◽  
pp. 1135-1140 ◽  
Author(s):  
Jason Qian ◽  
Zhi-xiang Lu ◽  
Christopher P. Mancuso ◽  
Han-Ying Jhuang ◽  
Rocío del Carmen Barajas-Ornelas ◽  
...  
Keyword(s):  
Food Safety ◽  
Nucleic Acid ◽  
High Resolution ◽  
Human Health ◽  
Nucleic Acid Detection ◽  
Single Spore ◽  
Detection Assay ◽  
Wide Range ◽  
Fundamental Challenge ◽  
Microbial System

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.

scholarly journals Indirect evolution of social fitness inequalities and facultative social exploitation

2018 ◽  
Vol 285 (1875) ◽  
pp. 20180054 ◽  
Author(s):  
Ramith R. Nair ◽  
Francesca Fiegna ◽  
Gregory J. Velicer
Keyword(s):  
Social Interaction ◽  
Experimental Evolution ◽  
Natural Populations ◽  
Spore Production ◽  
Fruiting Bodies ◽  
Cooperative Development ◽  
Indirect Evolution ◽  
Developmental Contexts ◽  
Selection For ◽  
Mixed Groups

Microbial genotypes with similarly high proficiency at a cooperative behaviour in genetically pure groups often exhibit fitness inequalities caused by social interaction in mixed groups. Winning competitors in this scenario have been referred to as ‘cheaters’ in some studies. Such interaction-specific fitness inequalities, as well as social exploitation (in which interaction between genotypes increases absolute fitness), might evolve due to selection for competitiveness at the focal behaviour or might arise non-adaptively due to pleiotropy, hitchhiking or genetic drift. The bacterium Myxococcus xanthus sporulates during cooperative development of multicellular fruiting bodies. Using M. xanthus lineages that underwent experimental evolution in allopatry without selection on sporulation, we demonstrate that interaction-specific fitness inequalities and facultative social exploitation during development readily evolved indirectly among descendant lineages. Fitness inequalities between evolved genotypes were not caused by divergence in developmental speed, as faster-developing strains were not over-represented among competition winners. In competitions between ancestors and several evolved strains, all evolved genotypes produced more spores than the ancestors, including losers of evolved-versus-evolved competitions, indicating that adaptation in non-developmental contexts pleiotropically increased competitiveness for spore production. Overall, our results suggest that fitness inequalities caused by social interaction during cooperative processes may often evolve non-adaptively in natural populations.

scholarly journals on the relevance of cognitive neuroscience for community of inquiry

2019 ◽  
Vol 15 ◽  
pp. 01-19
Author(s):  
Mark Leonard Weinstein ◽  
Dan Fisherman
Keyword(s):  
Critical Thinking ◽  
Cognitive Neuroscience ◽  
Community Of Inquiry ◽  
Deep Roots ◽  
Educational Thought ◽  
Self Reflection ◽  
Cooperative Development ◽  
Wide Range ◽  
The Face ◽  
Emotion And Memory

Community of inquiry is most often seen as a dialogical procedure for the cooperative development of reasonable approaches to knowledge and meaning. This reflects a deep commitment to normatively based reasoning that is pervasive in a wide range of approaches to critical thinking and argument, where the underlying theory of reasoning is logic driven, whether formal or informal.  The commitment to normative reasoning is deeply historical reflecting the fundamental distinction between reason and emotion. Despite the deep roots of the distinction and its canonization in current educational thought, contemporary cognitive neuroscience presents a fundamental challenge to the viability of the distinction and thus to any effort that sees education for reasonable judgment to be based on the remediation of cognition in isolation from its roots in the emotions. Cognitive neuroscience looks at the deep connections between emotion and memory, information retrieval, and resistance to refutation. This conforms with earlier studies in experimental psychology, which showed resistance to changing beliefs in the face of evidence, including evidence based on personal experience. This paper will look at the recent research including speculations from neurological modeling that shows the depth of connection between, emotions, memory and reasoning. It will draw implications for dialogic thinking within a community of inquiry including systematic self-reflection as an essential aspect of critical thinking.  

Forensic microbial system for high-resolution object provenance

2020 ◽  
Author(s):  
Jason Qian ◽  
Zhi-xiang Lu ◽  
Christopher P. Mancuso ◽  
Han-Ying Jhuang ◽  
Rocío del Carmen Barajas-Ornelas ◽  
...  
Keyword(s):  
Food Safety ◽  
High Resolution ◽  
Human Health ◽  
Single Spore ◽  
Wide Range ◽  
Fundamental Challenge ◽  
Microbial System

AbstractMapping where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes offers the potential to cheaply and sensitively determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under one hour at meter-scale resolution and near single spore sensitivity, and that can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, facilitating its implementation in a wide range of applications.

scholarly journals Robust gene expression control in human cells with a novel universal TetR aptamer splicing module

2019 ◽  
Vol 47 (20) ◽  
pp. e132-e132 ◽  
Author(s):  
Adam A Mol ◽  
Florian Groher ◽  
Britta Schreiber ◽  
Ciaran Rühmkorff ◽  
Beatrix Suess
Keyword(s):  
Gene Expression ◽  
Synthetic Biology ◽  
Dynamic Range ◽  
Intron Retention ◽  
Human Cells ◽  
Fine Tuning ◽  
Genomic Context ◽  
Mammalian Cell Lines ◽  
Gene Expression Control ◽  
Wide Range

Abstract Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.

Bioflocculation production from lower-molecular fatty acids as a novel strategy for utilization of sludge digestion liquor

2001 ◽  
Vol 44 (10) ◽  
pp. 237-243 ◽  
Author(s):  
M. Fujita ◽  
M. Ike ◽  
J.-H. Jang ◽  
S.-M. Kim ◽  
T. Hirao
Keyword(s):  
Fatty Acids ◽  
Batch Cultivation ◽  
Innovative Strategy ◽  
Sludge Digestion ◽  
Flocculating Activity ◽  
Wide Range ◽  
Natural Isolates ◽  
Novel Strategy ◽  
Fed Batch Cultivation ◽  
Logarithmic Growth

We propose the bioproduction of a bioflocculant from lower-molecular fatty acids as an innovative strategy for utilizing waste sludge digestion liquor. Fundamental studies on the production, characterization and application of a novel bioflocculant were performed. Citrobacter sp. TKF04 was screened out of 1,564 natural isolates as a bacterial strain capable of a bioflocculant from acetic and propionic acids. TKF04 produced the bioflocculant during the logarithmic growth in the batch cultivation, and it could be recovered from the culture supernatant by ethanol precipitation. The fed-batch cultivation with feeding of acetic acid: ammonium 10;1 (mole) to maintain pH 8.5 led to the hyper-production of the bioflocculant. The bioflocculant was found to be effective for flocculating a kaolin suspension, when added at a final concentration of 1-10 mg/l, over a wide range of pHs (2-8) and temperatures (3-95°C), while the addition of cations was not required. It could flocculate a variety of inorganic and organic suspended particles including kaolin, diatomite, bentonite, activated carbon, soil and activated sludge. These indicated that the bioflocculant possesses flocculating activity comparable or superior to that of synthetic flocculants. The bioflocculation was identified as a chitosan-like biopolymer.

scholarly journals Continental-scale gene flow prevents allopatric divergence of pelagic freshwater bacteria

2021 ◽  
Author(s):  
Matthias Hoetzinger ◽  
Alexandra Pitt ◽  
Andrea Huemer ◽  
Martin W Hahn
Keyword(s):  
Gene Flow ◽  
Regional Scale ◽  
Geographic Distance ◽  
Spatial Distance ◽  
Widespread Species ◽  
Continental Scale ◽  
Freshwater Bacteria ◽  
Wide Range ◽  
Allopatric Divergence ◽  
Open Question

Abstract Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for microbes with less strict habitat requirements are scarce. Furthermore, it has only recently been recognized that homologous recombination among conspecific individuals provides species coherence in a wide range of prokaryotes. Recombination barriers thus may define prokaryotic species boundaries, yet, the extent to which geographic distance between populations gives rise to such barriers is an open question. Here, we investigated gene flow and population structure in a widespread species of pelagic freshwater bacteria, Polynucleobacter paneuropaeus. Through comparative genomics of 113 conspecific strains isolated from freshwater lakes and ponds located across a North-South range of more than 3000 km, we were able to reconstruct past gene flow events. The species turned out to be highly recombinogenic as indicated by significant signs of gene transfer and extensive genome mosaicism. While genomic differences increased with spatial distance on a regional scale (< 170 km), such correlations were mostly absent on larger scales up to 3400 km. We conclude that allopatric divergence in European P. paneuropaeus is minor, and that effective gene flow across the sampled geographic range in combination with a high recombination efficacy maintains species coherence.

scholarly journals Metabolic manipulation by Pseudomonas fluorescens: a powerful stratagem against oxidative and metal stress

2020 ◽  
Vol 69 (3) ◽  
pp. 339-346 ◽  
Author(s):  
Alex MacLean ◽  
Anondo Michel Bley ◽  
Varun P. Appanna ◽  
Vasu D. Appanna
Keyword(s):  
Pseudomonas Fluorescens ◽  
Metabolic Networks ◽  
Value Added ◽  
Metal Stress ◽  
Fine Tuning ◽  
Content Type ◽  
Wide Range ◽  
Microbial System ◽  
Central Characteristic ◽  
Living Organisms

Metabolism is the foundation of all living organisms and is at the core of numerous if not all biological processes. The ability of an organism to modulate its metabolism is a central characteristic needed to proliferate, to be dormant and to survive any assault. Pseudomonas fluorescens is bestowed with a uniquely versatile metabolic framework that enables the microbe to adapt to a wide range of conditions including disparate nutrients and toxins. In this mini-review we elaborate on the various metabolic reconfigurations evoked by this microbial system to combat reactive oxygen/nitrogen species and metal stress. The fine-tuning of the NADH/NADPH homeostasis coupled with the production of α-keto-acids and ATP allows for the maintenance of a reductive intracellular milieu. The metabolic networks propelling the synthesis of metabolites like oxalate and aspartate are critical to keep toxic metals at bay. The biochemical processes resulting from these defensive mechanisms provide molecular clues to thwart infectious microbes and reveal elegant pathways to generate value-added products.

Strain Improvement of Trichoderma spp. Through Two Steps Protoplast Fusion for Cellulase Production Enhancement

2020 ◽  
Author(s):  
Zahra Papzan ◽  
Mojegan Kowsari ◽  
Mohammad Javan-Nikkhah ◽  
Amir Mirzadi Gohari ◽  
M. Carmen Limón
Keyword(s):  
Protoplast Fusion ◽  
Strain Improvement ◽  
Cellulase Activity ◽  
Cellulase Production ◽  
Mrna Levels ◽  
Hybrid Strain ◽  
Trichoderma Spp ◽  
Wide Range ◽  
Natural Isolates ◽  
Rut C30

Fungal protoplast fusion is an approach to introduce novel characteristics into industrially important strains. Cellulases, essential enzymes with a wide range of biotechnological applications, are produced by many species of the filamentous fungi Trichoderma. In this study, a collection of 60 natural isolates have been screened for Avicel and CMC degradation, and two cellulase producers of Trichoderma virens and Trichoderma harzianum were used for protoplast fusion. One of resulting hybrids with an improvement in cellulase activity, C1-3, was fused with the hyper producer Trichoderma reesei Rut-C30. A new selected hybrid, F7, increased its cellulase activity 1.8 and 5 times in comparison with Rut-C30 and C1-3, respectively. The increases in enzyme activity correlated with an upregulation of cellulolytic genes cbh1, cbh2, egl3, and bgl1 in the parents. Amount of mRNA of cbh1 and cbh2 in F7 resembled Rut-C30 while the bgl1 mRNA levels were similar to C1-3. AFLP fingerprinting and GC-MS analysis represented variations in parental strains and fusants. In conclusion, results demonstrate that a 3-interspecific hybrid strain has been isolated with improved characteristics for cellulase degradation showing genetic polymorphisms and differences in the volatile profile which suggests reorganizations at genetic level.

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