A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

Compant, Stéphane; Samad, Abdul; Faist, Hanna; Sessitsch, Angela

doi:10.1016/j.jare.2019.03.004

Cited by 974 publications

(713 citation statements)

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“…Describing the core microbiota is important for understanding the stable and consistent components across an array of complex and variable microbial assemblages (Shade & Handelsman, ). The core microbiota potentially comprises keystone taxa playing crucial roles in the functionality of a specific sample type (Compant, Samad, Faist, & Sessitsch, ). In our study, we used the package microbiome (Lahti & Shetty, ) to detect core ASVs at multiple scales (Figure ).…”

Section: Methodsmentioning

confidence: 99%

“…Core ASVs from a sample type were present in at least 70% of all the samples from that sample type. The comparison of abundance dispersion in white water environments for the guts of both species could not be computed, as only one core taxon was identified in those communities (see The core microbiota potentially comprises keystone taxa playing crucial roles in the functionality of a specific sample type (Compant, Samad, Faist, & Sessitsch, 2019). In our study, we used the package microbiome (Lahti & Shetty, 2017) to detect core ASVs at multiple scales ( Figure 4).…”

Section: Statistical Analysis Of Sequence Variantsmentioning

confidence: 99%

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Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients

et al. 2019

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The world's richest freshwater fish community thrives in gradients of contrasting environments in Amazonia, ranging from ion‐poor acidic black waters, to ion‐rich circumneutral white waters. These hydrochemical gradients structure Amazonian fish assemblages via ecological speciation events. Fish bacterial communities contain an important genetic heritage essential for their hosts' survival and are also involved in adaptive divergence via niche adaptation processes, but the extent to which they evolve in response to hydrochemical gradients in Amazonia is unknown. Here we investigated bacterial communities (gut and skin mucus) of two ecologically and phylogenetically divergent host species (Mesonauta festivus and Serrasalmus rhombeus) distributed throughout these hydrochemical gradients. The goal was to characterize intra‐ and interspecific Amazonian fish microbiome variations across multiple scales. Using a 16S metabarcoding approach, we investigated the microbiota of 43 wild M. festivus, 32 S. rhombeus and seven water samples, collected at seven sampling sites encompassing both water colours. Taxonomical structures of bacterial communities from both host species were significantly correlated to the environmental continua of magnesium, sodium, dissolved organic carbon, calcium, dissolved O2, pH, potassium, hardness and chloride. Analysis of discriminating features in community structures across multiple scales demonstrated intra‐ and interspecific structural parallelisms in the response to the hydrochemical gradients. Together, these parallelisms suggest the action of selection on bacterial community structures along Amazonian hydrochemical gradients. Functional approaches along with reciprocal transplant experiments will provide further insights on the potential contribution of Amazonian fish microbiomes in host adaptation and ecological speciation events.

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Section: Methodsmentioning

confidence: 99%

Section: Statistical Analysis Of Sequence Variantsmentioning

confidence: 99%

Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients

et al. 2019

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“…In plants, microbial community structure on the phyllosphere is correlated with key plant growth characteristics, including wood density, leaf mass per area and mortality (Kembel et al, 2014). Similarly, soil microbial diversity and structure have been shown to strongly impact plant biomass production, plant-plant interactions, and plays a role in maintaining species diversity (Compant, Samad, Faist, & Sessitsch, 2019;Yang, Wagg, Veresoglou, Hempel, & Rillig, 2018). The contribution of microorganisms to plant growth through mycorrhizal fungi, nitrogen fixing bacteria, and the wider above-and below-ground microbiome, is well known, and there is a growing appreciation for additional roles in resistance to biotic and abiotic stressors (Vandenkoornhuyse, Quaiser, Duhamel, Van, & Dufresne, 2015).…”

Section: Introductionmentioning

confidence: 99%

Conserving the holobiont

et al. 2020

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Organismal biology has undergone a dramatic paradigm shift in the last decade. The realization that host cells and genes are outnumbered by symbiotic microbial cells and their genes has forced us to rethink our focus on ‘individuals’. It is also becoming increasingly clear that the ecology and biology of animals and plants are intimately connected with their microbial partners. In the context of conserving functioning species, such revelatory insights beg the question—what exactly should we be trying to conserve? Here, we review how an understanding of host–microbe interactions can benefit conservation biology. We propose a way forward for conservation biologists, to gather evidence of the potential effects of changes to plant and animal microbiomes, and to incorporate the holobiont concept into applied conservation practice. In humans, microbes influence physiology, health, behaviour and psychology. In animals and plants, microbes similarly influence critically important components of health, communication and (in animals) behaviour. Together, the animal or plant and all of its associated micro‐organisms are termed the holobiont. At the same time, humans are now the strongest evolutionary force on the planet, causing global change at unprecedented scale. We know that microbial diversity in humans has been compromised in urban societies, with a growing list of consequences for health and function. While we still have limited evidence for similar effects in plants and animals, anthropogenic factors that affect diversity are also likely to affect animal and plant microbiomes, with similar associated effects on host function and health. Microbiome research is still in its relative infancy, particularly in its application to plants and animals, yet the tools are becoming more widely available and affordable. Forward‐looking conservation biologists could harness such tools and apply them to the study of plant and animal microbiomes with the goal of understanding which microbiota might be required to ensure future viability of conserved host populations. For now, the precautionary principle applies. We suggest that, to meaningfully and effectively conserve a species, we must also consider how to conserve the bacteria, viruses, fungi and other symbionts intimately associated with that macro‐organism. A free Plain Language Summary can be found within the Supporting Information of this article.

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“…This effect may be due to adverse effect of environmental conditions or autochthonic microorganisms on gene expression in microbial cells (Baez-Rogelio et al, 2016) or low competitiveness of microorganisms used as biofertilizers, i.e.they may be outgrown by autochthonic ones. This is why “plant microbiome” was proposed as new generation of inoculants (Compant et al, 2019). Inoculation of crops with microbiome and organic matter present in lyophilized plant roots seems to be a better solution to enrich microbial biodiversity of soil and crops with new endophytes.…”

Section: Introductionmentioning

confidence: 99%

Effect of osmoprotectants on the survival of bacterial endophytes in lyophilized beet roots

Szymańska

Sikora

Hrynkiewicz

et al. 2019

Preprint

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The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fits into sustainable agricultural technologies ideas. We aimed to: (i) assess the diversity of endophytic bacteria in beet roots and (ii) determine the influence of osmoprotectants addition during lyophilization on bacterial density, viability, salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fluorescence microscopy and flow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines physicochemical rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive effect on bacterial community salt stress tolerance, viability and density. Trehalose improves these parameters more effectively than ectoine, moreover its use is economically advantageous.

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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

Abstract: Graphical abstract

Cited by 974 publications

References 115 publications

Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients

Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients

Conserving the holobiont

Effect of osmoprotectants on the survival of bacterial endophytes in lyophilized beet roots

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