A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

Armanhi, Jaderson Silveira Leite; Souza, Rafael Soares Correa de; Damasceno, Natália de Brito; Araújo, Laura Migliorini de; Imperial, Juan; Arruda, Paulo

doi:10.3389/fpls.2017.02191

Cited by 106 publications

(95 citation statements)

References 75 publications

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“…Due to their absence in the bulk soil, we can speculate that members of the Moraxellaceae family are true endophytes that can be transmitted from the seeds to the root endosphere. This family has been previously discovered in root environments and several genera of the Moraxellaceae are known to promote plant growth [45][46][47]. Secondly, the family Flavobacteriaceae was detected in the root endosphere of both soil-and in vitro-grown maize and additionally, also in the bulk soil samples.…”

Section: Discussionmentioning

confidence: 83%

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Beirinckx

Viaene²,

Haegeman³

et al. 2020

Microbiome

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Background: When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. Results: We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. Conclusions: Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions.

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Section: Discussionmentioning

confidence: 83%

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Beirinckx

Viaene²,

Haegeman³

et al. 2020

Microbiome

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“…Members of these dominant groups, named the core microbiome, can be incorporated in SynComs, thus preventing the lack of efficiency and prevalence observed in situations where strains are outcompeted by naturally occurring microbiota. Notably, studies using both abundant and prevalent core microbes in SynComs have shown efficient colonization and beneficial effects such as plant defense against pathogens and root growth ( Niu et al, 2017 ; Armanhi et al, 2018 ). These studies confirm that core microbial groups are extremely efficient at colonizing plants, highlighting that dominant groups are likely involved in functions important for plant growth and survival.…”

Section: Identifying Relevant Microbes With Key Traits For Stable Andmentioning

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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“…S2). To verify their functions, new cultivation and screening strategies, such as optimization of the culture medium (54) and conditions (55) or multiple in vitro tests involved in different suppressive mechanisms, should be considered.…”

Section: Discussionmentioning

confidence: 99%

Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance

Guo

et al. 2019

Appl Environ Microbiol

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Crown gall disease caused by Agrobacterium tumefaciens severely impacts the production of peach and other fruit trees. Several peach cultivars are partially resistant to A. tumefaciens, but little is known about the roles of endophytic microbiota in disease resistance. In the present study, the endophytic bacterial communities of resistant and susceptible peach cultivars "Honggengansutao" and "Okinawa" were analyzed using universal 16S rRNA gene amplicon sequencing in parallel with the cultivation and characterization of bacterial isolates. A total of 1,357,088 high-quality sequences representing 3,160 distinct operational taxonomic units (OTUs; Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes) and 1,200 isolates of 20 genera and 305 distinct ribotypes were collected from peach roots and twigs. It was found that factors including plant developmental stage, cultivar, and A. tumefaciens invasion strongly influenced the peach endophytic communities. The community diversity of endophytic bacteria and the abundance of culturable bacteria were both higher in the roots of the resistant cultivar, particularly after inoculation. Strikingly, the pathogen antagonists Streptomyces and Pseudomonas in roots and Rhizobium in twigs were most frequently detected in resistant plants. Our results suggest that the higher abundance and diversity of endophytic bacteria and increased proportions of antagonistic bacteria might contribute to the natural defense of the resistant cultivar against A. tumefaciens. This work reveals the relationships between endophytic bacteria and disease resistance in peach plants and provides important information for microbiome-based biocontrol of crown gall disease in fruit trees. IMPORTANCE Agrobacterium tumefaciens as the causal agent of peach crown gall disease can be controlled by planting resistant cultivars. This study profiles the endophytic bacteria in susceptible and resistant peach cultivars, advancing our understanding of the relationships between endophytic bacterial communities and peach crown gall disease, with potential implications for other complex microbiome-plantpathogen interactions. The resistant cultivar may defend itself by increasing the diversity and abundance of beneficial endophytic bacteria. The antagonists identified among the genera Streptomyces, Pseudomonas, and Rhizobium may have application potential for biocontrol of crown gall disease in fruit trees.

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A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

Cited by 106 publications

References 75 publications

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

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

Insight into the Bacterial Endophytic Communities of Peach Cultivars Related to Crown Gall Disease Resistance

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