The Inherent Conflicts in Developing Soil Microbial Inoculants

Kaminsky, Laura M.; Trexler, Ryan V.; Malik, Rondy J.; Hockett, Kevin L.; Bell, Terrence H.

doi:10.1016/j.tibtech.2018.11.011

Cited by 241 publications

(189 citation statements)

References 95 publications

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“…SynComs are small consortia of microorganisms designed to mimic, at some scale, the observed function and structure of the microbiome in natural conditions. The rationale is to reduce the complexity of the microbial community while still preserving some of the original interactions between microbes and hosts, providing a repertoire of functions that would not be achievable by a single microbe ( Qin et al, 2016 ; Niu et al, 2017 ; Vorholt et al, 2017 ; Kaminsky et al, 2019 ). In addition to broadening the scope of features and metabolites, SynComs may also increase community stability through synergistic interactions between their members ( McCarty and Ledesma-Amaro, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

2020

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Plants teem with microorganisms, whose tremendous diversity and role in plant–microbe interactions are being increasingly explored. Microbial communities create a functional bond with their hosts and express beneficial traits capable of enhancing plant performance. Therefore, a significant task of microbiome research has been identifying novel beneficial microbial traits that can contribute to crop productivity, particularly under adverse environmental conditions. However, although knowledge has exponentially accumulated in recent years, few novel methods regarding the process of designing inoculants for agriculture have been presented. A recently introduced approach is the use of synthetic microbial communities (SynComs), which involves applying concepts from both microbial ecology and genetics to design inoculants. Here, we discuss how to translate this rationale for delivering stable and effective inoculants for agriculture by tailoring SynComs with microorganisms possessing traits for robust colonization, prevalence throughout plant development and specific beneficial functions for plants. Computational methods, including machine learning and artificial intelligence, will leverage the approaches of screening and identifying beneficial microbes while improving the process of determining the best combination of microbes for a desired plant phenotype. We focus on recent advances that deepen our knowledge of plant–microbe interactions and critically discuss the prospect of using microbes to create SynComs capable of enhancing crop resiliency against stressful conditions.

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Section: Introductionmentioning

confidence: 99%

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

2020

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“…In addition, secondary metabolite production by endophytes is generally down‐regulated when cultured individually but activated in response to other microbes (Schroeckh et al, ; Suryanarayanan, ), indicating complex and bi‐directional interactions between members of the phyllosphere microbiome. Thus, co‐culturing such microbes, potentially identified through co‐occurrence hubs, may help guide the development of consortium‐based approaches to probiotic development, which may be more effective than single‐species probiotics (Antwis & Harrison, ; Kaminsky, Trexler, Malik, Hockett, & Bell, ; Schulz et al, ).…”

Section: Discussionmentioning

confidence: 99%

Complex associations between cross‐kingdom microbial endophytes and host genotype in ash dieback disease dynamics

et al. 2019

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1. Tree pathogens are a major threat to forest ecosystems. Conservation management strategies can exploit natural mechanisms of resistance, such as tree genotype and host-associated microbial communities. However, fungal and bacterial communities are rarely looked at in the same framework, particularly in conjunction with host genotype. Here, we explore these relationships and their influence on ash dieback disease, caused by the pathogen Hymenoscyphus fraxineus, in European common ash trees.2. We collected leaves from UK ash trees and used microsatellite markers to genotype trees, quantitative PCR to quantify H. fraxineus infection load and ITS and 16S rRNA amplicon sequencing to identify fungal and bacterial communities, respectively.3. There was a significant association between H. fraxineus infection intensity and ash leaf fungal and bacterial community composition. Higher infection levels were positively correlated with fungal community alpha-diversity, and a number of fungal and bacterial genera were significantly associated with infection presence and intensity. Under higher infection loads, leaf microbial networks were characterized by stronger associations between fewer members than those associated with lower infection levels. Together these results suggest that H. fraxineus disrupts stable endophyte communities after a particular infection threshold is reached, and may enable proliferation of opportunistic microbes. We identified three microbial genera associated with an absence of infection, potentially indicating an antagonistic relationship with H. fraxineus that could be utilized in the development of anti-pathogen treatments. 4. Host genotype did not directly affect infection, but did significantly affect leaf fungal community composition. Thus, host genotype could have the potential to indirectly affect disease susceptibility through genotype × microbiome interactions, and should be considered when selectively breeding trees. 5.Synthesis. We show that the diversity, composition and network structure of ash leaf microbial communities are associated with the severity of infection from ash dieback disease, with evidence of disease-induced dysbiosis. We also show that host genotype influences leaf fungal community composition, but does not directly influence tree infection. These findings help to elucidate relationships between host genetics, the microbiome and a tree pathogen, highlighting potential resistance mechanisms and possible co-infection concerns that could inform ash tree management. K E Y W O R D S amplicon sequencing, bacteria, Fraxinus excelsior, fungi, genetic diversity, Hymenoscyphus fraxineus, microbiome, tree pathogen | 293 Journal of Ecology GRIFFITHS eT al.

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“…The application of microbial inoculants to the soil in order to modify certain processes and functions is a practice that has grown in popularity over the past few years [8,9]. While results obtained through function screening and cultivation in laboratory conditions are promising, the large-scale application in the field presents challenges in the establishment, persistence, and performance of microbes [10]. Influencing the composition and structure of the rhizosphere-associated microbial community by inoculating indigenous or allochthonous microorganisms is a promising research avenue.…”

Section: Introductionmentioning

confidence: 99%

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments

Dagher

Providencia²,

Pitre

et al. 2020

Microorganisms

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Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.

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The Inherent Conflicts in Developing Soil Microbial Inoculants

Cited by 241 publications

References 95 publications

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

Complex associations between cross‐kingdom microbial endophytes and host genotype in ash dieback disease dynamics

Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments

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