Better together: engineering and application of microbial symbioses

Hays, Stephanie G.; Patrick, William G; Ziesack, Marika; Oxman, Neri; Silver, Pamela A.

doi:10.1016/j.copbio.2015.08.008

Cited by 247 publications

(168 citation statements)

References 88 publications

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“…altered the post-embryonic root development in Arabidopsis that stimulated production of more lateral roots and root hairs and helped the plants perform better under water- and nutrient-limited conditions (Zamioudis et al, 2013). These results indicate that there is better performance of bacteria when they are applied in a consortium underlining their network mode of activity (Hays et al, 2015) in regulating plant fitness. Now, the plant-microbiome relationship via ‘holobiont’ concept is not only restricted to production and protection applications in plants but is also expanding into the realm of plant breeding.…”

Section: Microbes Work In Network Mode To Regulate Plant Fitnessmentioning

confidence: 87%

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

2016

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“No plant is an island too…”Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the ‘plant microbiome,’ form the holobiome which is now considered as unit of selection: ‘the holobiont.’ The ‘plant microbiome’ not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom–up approach to co-propagate the co-evolved, the plant along with the target microbiome, through – (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method – for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.

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Section: Microbes Work In Network Mode To Regulate Plant Fitnessmentioning

confidence: 87%

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

2016

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“…However, there is also the promising potential to use an engineered consortium [53][54][55] for similar molecular assembly. These complementary synthetic systems have already been introduced.…”

Section: Discussionmentioning

confidence: 99%

Modeling information exchange between living and artificial cells

et al. 2017

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Background: The tools of synthetic biology have enabled researchers to explore multiple scientific phenomena by directly engineering signaling pathways within living cells and artificial protocells. Here, we explored the potential for engineered living cells themselves to assemble signaling pathways for non-living protocells. This analysis serves as a preliminary investigation into a potential origin of processes that may be utilized by complex living systems. Specifically, we suggest that if living cells can be engineered to direct the assembly of genetic signaling pathways from genetic biomaterials in their environment, then insight can be gained into how naturally occurring living systems might behave similarly.Methods: To this end, we have modeled and simulated a system consisting of engineered cells that control the assembly of DNA monomers on microparticle scaffolds. These DNA monomers encode genetic circuits, and therefore, these microparticles can then be encapsulated with minimal transcription and translation systems to direct protocell phenotype. The modeled system relies on multiple previously established synthetic systems and then links these together to demonstrate system feasibility.Results: In this specific model, engineered cells are induced to synthesize biotin, which competes with biotinylated, circuit-encoding DNA monomers for an avidinized-microparticle scaffold. We demonstrate that multiple synthetic motifs can be controlled in this way and can be tuned by manipulating parameters such as inducer and DNA concentrations. Conclusions:We expect that this system will provide insight into the origin of living systems as well as serve as a tool for engineering living cells that assemble complex biomaterials in their environment.

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“…It may also be possible to design and test systems for predation, parasitism, commensalism and symbiosis in artificial multicellular 'organisms' to test principles of development at the ecosystem scale. Synthetic biological approaches to cooperation and symbiosis have already been applied to microorganisms (Shou et al, 2007;Grosskopf and Soyer, 2014;Hays et al, 2015), showing that, in principle, this type of work is possible.…”

Section: Towards Synthetic Developmentmentioning

confidence: 99%

Using synthetic biology to explore principles of development

Davies

2017

Development

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Developmental biology is mainly analytical: researchers study embryos, suggest hypotheses and test them through experimental perturbation. From the results of many experiments, the community distils the principles thought to underlie embryogenesis. Verifying these principles, however, is a challenge. One promising approach is to use synthetic biology techniques to engineer simple genetic or cellular systems that follow these principles and to see whether they perform as expected. As I review here, this approach has already been used to test ideas of patterning, differentiation and morphogenesis. It is also being applied to evo-devo studies to explore alternative mechanisms of development and 'roads not taken' by natural evolution.

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Better together: engineering and application of microbial symbioses

Cited by 247 publications

References 88 publications

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

Modeling information exchange between living and artificial cells

Using synthetic biology to explore principles of development

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