Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

Hu, Jie; Wei, Zhong; Friman, Ville‐Petri; Gu, Siyi; Wang, Xiao Fang; Eisenhauer, Nico; Yang, Tian; Ma, Jing; Shen, Qi; Xu, Yang; Jousset, Alexandre

doi:10.1128/mbio.01790-16

Cited by 307 publications

(300 citation statements)

References 43 publications

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“…), the survival of the biocontrol agent (Hu et al . ) and the interactive effects within microbiomes (Thomas & Sekhar ). To develop more consistent biocontrol applications, effort should be put on studying how seasonal and spatial variation in abiotic and biotic soil properties affect the stability and strength of biocontrol agent–pathogen species interactions.…”

Section: Discussionmentioning

confidence: 99%

“…For example, biocontrol outcomes could vary between different fields depending on the soil type and the given microbial community composition, which could considerably affect the biocontrol agent survival (Hu et al . ) and antimicrobial activity in the vicinity of the target host (Tyc et al . ).…”

Section: Discussionmentioning

confidence: 99%

“…; Hu et al . ), more research is still needed to quantify the strength of microbial competition in more natural conditions (e.g. in soil microcosms) (Gomez & Buckling ).…”

Section: Discussionmentioning

confidence: 99%

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Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature‐mediated changes in bacterial competitive interactions

Wei

Huang

Yang

et al. 2017

Journal of Applied Ecology

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Summary Microbe‐based biocontrol applications hold the potential to become an efficient way to control plant pathogen disease outbreaks in the future. However, their efficiency is still very variable, which could be due to their sensitivity to the abiotic environmental conditions.Here, we assessed how environmental temperature variation correlates with ability of Ralstonia pickettii, an endophytic bacterial biocontrol agent, to suppress the Ralstonia solanacearum pathogen during different tomato crop seasons in China.We found that suppression of the pathogen was highest when the seasonal mean temperatures were around 20 °C and rapidly decreased with increasing mean crop season temperatures. Interestingly, low levels of disease incidence did not correlate with low pathogen or high biocontrol agent absolute densities. Instead, the biocontrol to pathogen density ratio was a more important predictor of disease incidence levels between different crop seasons. To understand this mechanistically, we measured the growth and strength of competition between the biocontrol agent and the pathogen over a naturally occurring temperature gradient in vitro. We found that the biocontrol strain grew relatively faster at low temperature ranges, and the pathogen at high temperature ranges, and that similar to field experiments, pathogen suppression peaked at 20 °C.Together, our results suggest that temperature‐mediated changes in the strength of bacterial competition could potentially explain the variable R. solanacearum biocontrol outcomes between different crop seasons in China. Synthesis and applications. Our results suggest that abiotic environmental conditions, such as temperature, can affect the efficacy of biocontrol applications. Thus, in order to develop more consistent biocontrol applications in the future, we might need to find and isolate bacterial strains that can retain their functionality regardless of the changing environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature‐mediated changes in bacterial competitive interactions

Wei

Huang

Yang

et al. 2017

Journal of Applied Ecology

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“…In other cases, however, consortia were equal to, or worse than, some individual strains tested, as evidenced by the growth of grapevines under drought stress [23]. Consortia can consist of either closely related strains used to expand the niche breadth of a certain trait [54,55], or of distantly related strains providing PGP via different mechanisms, thus contributing to an overall additive effect [59]. However, increasing strain richness, for example within the biocontrol species Pseudomonas fluorescens , can cause community collapse and subsequent loss of plant protection [60].…”

Section: Diversity Of the Inoculummentioning

confidence: 99%

Understanding and exploiting plant beneficial microbes

Finkel

Castrillo

Paredes

et al. 2017

Current Opinion in Plant Biology

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After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.

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“…Understanding differences between pathogen colonization and evolution in natural versus agricultural systems 377 may similarly lead to innovations that reduce pathogen pressure in agriculture (Hu et al, 2016). Much can be 378 learned about the course of pathogen colonization and evolution by examining pathogen population diversity 379…”

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confidence: 99%

Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

Karasov

Almario

Friedemann

et al. 2018

Preprint

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SummaryCrop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine 20 whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site 21 survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage 22 corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed 23 this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct 24 pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are 25 differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages 26indicates that in contrast to crop systems, no single strain has been able to overtake these A. thaliana 27 populations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in 28 wild hosts may be more complex than those in agricultural systems. 29 Introduction 30In agricultural and clinical settings, pathogenic colonizations are frequently associated with expansions of single 31 or a few genetically identical microbial lineages (Butler et al., 2013; Cai et al., 2011;Kolmer, 2005; Park et al., 32 2015;Stukenbrock and McDonald, 2008; Yoshida et al., 2013). The conditions that lead to such epidemics-such 33 as reduced host genetic diversity (Zhu et al., 2000), absence of competing microbial communities (Brown et al., 34 2013) or high transmission rates (Park et al., 2015)-are, however, by no means a universal feature of 35 pathogenic infections. Instead, many, if not most, pathogens can colonize host populations that are both 36 genetically diverse and that can accommodate a diversity of other microbes (Barrett et al., 2009; Falkinham et 37 al., 2015;Woolhouse et al., 2001). 38Factors that drive pathogen success in such more complex situations are less well understood than for 39 clonal epidemics. For example, if a pathogen species persists at high numbers in non-host environments, does 40 each host become infected by a different pathogen strain? Or does a multitude of genetically distinct pathogens 41 infect each host? And do different colonizing strains use disparate mechanisms to become established even 42 within genetically similar host individuals? The answers to these questions inform on how (and if) a host 43 population can evolve partial or even complete pathogen resistance (Anderson and May, 1982; Barrett et al., 44 2009; Karasov et al., 2014a;Laine et al., 2011). Several studies over the past 20 years have attempted to infer 45 the distributions of non-epidemic pathogens in both host and non-host environments (Falkinham et al., 2015; 46 Wiehlmann et al., 2007). These studies, which have observed a range of different patterns, are unfortunately 47 often limited to the historic strains that are available, and the conclusions vary for different collections, even of 48 the same pathogen ...

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Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

Cited by 307 publications

References 43 publications

Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature‐mediated changes in bacterial competitive interactions

Seasonal variation in the biocontrol efficiency of bacterial wilt is driven by temperature‐mediated changes in bacterial competitive interactions

Understanding and exploiting plant beneficial microbes

Stability of association betweenArabidopsis thalianaandPseudomonaspathogens over evolutionary time scales

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