Pawnobiome: manipulation of the hologenome within one host generation and beyond

Voss, Jameson D.; León, Juan; Dhurandhar, Nikhil V.; Robb, Frank T.

doi:10.3389/fmicb.2015.00697

Cited by 20 publications

(23 citation statements)

References 55 publications

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“…Can shifts at the microbial community level act akin to shifts in allele frequencies in host genomes? Preliminary indications are that not only can this occur, but that we can capitalize on its occurrence by artificially selecting (i.e., microbiome engineering) holobiont phenotypes in applied contexts (12, 13).…”

Section: Main Textmentioning

confidence: 99%

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Theis

Dheilly

Klassen

et al. 2016

Preprint

107

141

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Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organizationwhat is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

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Section: Main Textmentioning

confidence: 99%

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Theis

Dheilly

Klassen

et al. 2016

Preprint

107

141

View full text Add to dashboard Cite

show abstract

“…Consequently, it is predicted that holobionts can rapidly evolve/ adapt through their microbiota by: (i) horizontal gene transfer among their existing microbiota, (ii) recruitment of new microbes from the environment, (iii) shifts in the relative abundance/gene expression of various members of the microbiota. These mechanisms are thought to enable holobionts to adapt within a single or a few generations (Voss et al, 2015;Rosenberg and Zilber-Rosenberg, 2016). It has recently been shown that the response of willows to stressful conditions (soil contamination) results in large shifts in the metatranscriptome of root and rhizosphere bacterial and fungal communities, but not in the plant root transcriptome (Gonzalez et al, 2018;Yergeau et al, 2018).…”

Section: Microbes As Hydrocarbon Degradersmentioning

confidence: 99%

Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation

Correa-García

Pande

Séguin

et al. 2018

Microbial Biotechnology

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SummaryPhytoremediation is a green and sustainable alternative to physico‐chemical methods for contaminated soil remediation. One of the flavours of phytoremediation is rhizoremediation, where plant roots stimulate soil microbes to degrade organic contaminants. This approach is particularly interesting as it takes advantage of naturally evolved interaction mechanisms between plant and microorganisms and often results in a complete mineralization of the contaminants (i.e. transformation to water and CO 2). However, many biotic and abiotic factors influence the outcome of this interaction, resulting in variable efficiency of the remediation process. The difficulty to predict precisely the timeframe associated with rhizoremediation leads to low adoption rates of this green technology. Here, we review recent literature related to rhizoremediation, with a particular focus on soil organisms. We then expand on the potential of rhizoremediation to be a model plant‐microbe interaction system for microbiome manipulation studies.

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“…However, getting to the relevant bacterial species and preparing their appropriate consortia is the main challenge here because of the complex nature of the microbe-plant interactions. By adopting artificial ecosystem selection method of microbiome transfer (Swenson et al, 2000; De Roy et al, 2014; Voss et al, 2015), strong evidence of heritable changes in drought tolerance in Arabidopsis thaliana (Zolla et al, 2013), alteration of flowering time in Arabidopsis thaliana genotypes, Brassica rapa (Panke-Buisse et al, 2014) and Boechera stricta (Wagner et al, 2014) have been reported. The findings of overlapping core-microbiome in sugarcane (Yeoh et al, 2015) and rice (Edwards et al, 2015) with those of Arabidopsis (Lundberg et al, 2012) give more hope for cross-compatibility of microbiome transfer with phylogenetically unrelated plant species.…”

Section: Artificial Ecosystem Selection Of Plant Microbiomementioning

confidence: 99%

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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Pawnobiome: manipulation of the hologenome within one host generation and beyond

Cited by 20 publications

References 55 publications

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation

Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

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