Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota

Cheng, Zhiqiang; Lei, Shaonan; Li, Ye; Huang, Wei; Ma, Rongqin; Xiong, Juan; Zhang, Ting; Jin, Lingyue; Haq, Hafeez Ul; Xu, Xiaohong; Tian, Baoyu

doi:10.3390/microorganisms8020170

Cited by 48 publications

(38 citation statements)

References 53 publications

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“…Complete information on unique and shared OTUs is available ( Supplementary Table S3 ). In comparison to our result, another study identified a bacterial tomato rhizosphere core microbiome composed of 68 orders using different tomato cultivars in a single soil, and 27 orders using a single tomato genotype in five soils ( Cheng et al, 2020 ).…”

Section: Resultscontrasting

confidence: 56%

Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources

et al. 2020

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The two-step model for plant root microbiomes considers soil as the primary microbial source. Active selection of the plant’s bacterial inhabitants results in a biodiversity decrease toward roots. We collected sixteen samples of in situ ruderal plant roots and their soils and used these soils as the main microbial input for single genotype tomatoes grown in a greenhouse. Our main goal was to test the soil influence in the structuring of rhizosphere microbiomes, minimizing environmental variability, while testing multiple plant species. We massively sequenced the 16S rRNA and shotgun metagenomes of the soils, in situ plants, and tomato roots. We identified a total of 271,940 bacterial operational taxonomic units (OTUs) within the soils, rhizosphere and endospheric microbiomes. We annotated by homology a total of 411,432 (13.07%) of the metagenome predicted proteins. Tomato roots did follow the two-step model with lower α-diversity than soil, while ruderal plants did not. Surprisingly, ruderal plants are probably working as a microenvironmental oasis providing moisture and plant-derived nutrients, supporting larger α-diversity. Ruderal plants and their soils are closer according to their microbiome community composition than tomato and its soil, based on OTUs and protein comparisons. We expected that tomato β-diversity clustered together with their soil, if it is the main rhizosphere microbiome structuring factor. However, tomato microbiome β-diversity was associated with plant genotype in most samples (81.2%), also supported by a larger set of enriched proteins in tomato rhizosphere than soil or ruderals. The most abundant bacteria found in soils was the Actinobacteria Solirubrobacter soli , ruderals were dominated by the Proteobacteria Sphingomonas sp. URGHD0057, and tomato mainly by the Bacteroidetes Ohtaekwangia koreensis , Flavobacterium terrae, Niastella vici , and Chryseolinea serpens. We calculated a metagenomic tomato root core of 51 bacterial genera and 2,762 proteins, which could be the basis for microbiome-oriented plant breeding programs. We attributed a larger diversity in ruderal plants roots exudates as an effect of the moisture and nutrient acting as a microbial harbor. The tomato and ruderal metagenomic differences are probably due to plant domestication trade-offs, impacting plant-bacteria interactions.

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Section: Resultscontrasting

confidence: 56%

Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources

et al. 2020

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“…The communities sequenced in this study were dominated by bacteria of the phyla Bacteroidetes and Proteobacteria. Other studies conducted on tomato plants report a community dominated by Proteobacteria [ 50 , 51 , 52 , 53 , 54 ] and Ascomycota, the dominant fungal phylum in this study [ 53 ]. In addition, Bacteroidetes have been observed previously in similar abundance in the tomato rhizosphere [ 51 , 54 ].…”

Section: Discussionsupporting

confidence: 56%

Organic Amendments Alter Soil Hydrology and Belowground Microbiome of Tomato (Solanum lycopersicum)

2021

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Manure-derived organic amendments are a cost-effective tool that provide many potential benefits to plant and soil health including fertility, water retention, and disease suppression. A greenhouse experiment was conducted to evaluate how dairy manure compost (DMC), dairy manure compost-derived vermicompost (VC), and dehydrated poultry manure pellets (PP) impact the tripartite relationship among plant growth, soil physiochemical properties, and microbial community composition. Of tomato plants with manure-derived fertilizers amendments, only VC led to vigorous growth through the duration of the experiment, whereas DMC had mixed impacts on plant growth and PP was detrimental. Organic amendments increased soil porosity and soil water holding capacity, but delayed plant maturation and decreased plant biomass. Composition of bacterial communities were affected more by organic amendment than fungal communities in all microhabitats. Composition of communities outside roots (bulk soil, rhizosphere, rhizoplane) contrasted those within roots (endosphere). Distinct microbial communities were detected for each treatment, with an abundance of Massilia, Chryseolinea, Scedosporium, and Acinetobacter distinguishing the control, vermicompost, dairy manure compost, and dehydrated poultry manure pellet treatments, respectively. This study suggests that plant growth is affected by the application of organic amendments not only because of the soil microbial communities introduced, but also due to a synergistic effect on the physical soil environment. Furthermore, there is a strong interaction between root growth and the spatial heterogeneity of soil and root-associated microbial communities.

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“…Rhizosphere microorganisms could contribute to plant health, growth and productivity (Cheng et al 2020; 6 Gene profiles of the bacterial community in P. ludlowii tissues and rhizosphere soil predicted using PICRUSt Mendes et al 2013). However, some important microbial groups, such as Pseudomonas and Bacillus, decreased with soil depth.…”

Section: Discussionmentioning

confidence: 99%

Analysis of endophytic and rhizosphere bacterial diversity and function in the endangered plant Paeonia ludlowii

Zhang

Hong

et al. 2020

Arch Microbiol

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Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii . Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii . This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.

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Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota

Cited by 48 publications

References 53 publications

Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources

Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources

Organic Amendments Alter Soil Hydrology and Belowground Microbiome of Tomato (Solanum lycopersicum)

Analysis of endophytic and rhizosphere bacterial diversity and function in the endangered plant Paeonia ludlowii

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