Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere

Chang, Jingjing; Shi, Shaohua; Tian, Lei; Leite, Márcio Fernandes Alves; Chang, Chunguang; Li, Ji; Ma, Lina; Tian, Chunjie; Kuramae, Eiko E.

doi:10.3390/microorganisms9010175

Cited by 10 publications

(8 citation statements)

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“…Domestication has been shown to alter the diversity of microbes in the rhizosphere of crops such as corn [45], tomato [46], wheat [47], and rice [48,49]. Chang et al [50] compared the bacterial communities of wild and domesticated rice genotypes and found that Frankiaceae was enriched in the rhizosphere of cultivated Oryza sativa but absent from the rhizosphere of wild Oryza rufipogon. This result highlights that unique microbes that are not recruited by wild relatives are enriched in the rhizosphere of domesticated cultivars.…”

Section: Discussionmentioning

confidence: 99%

“…Soil pH and electrical conductivity (EC) were measured in a suspension of soil in water at a ratio of 1:2.5 (w/v). Soil total nitrogen (TN), soil organic matter (SOM), available phosphorus (AP), and available potassium (AK) were measured by the Kjeldahl method, potassium dichromate volumetric method, NaHCO 3 extraction method and ammonium acetate extraction method, respectively, as described by Chang et al [50].…”

Section: Analysis Of Rhizosphere Soil Physical and Chemical Propertiesmentioning

confidence: 99%

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Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

et al. 2022

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Background The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. Results Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. Conclusion We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera.

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Section: Discussionmentioning

confidence: 99%

Section: Analysis Of Rhizosphere Soil Physical and Chemical Propertiesmentioning

confidence: 99%

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

et al. 2022

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“…8). Members of Xanthobacteraceae have been found to associate with the rhizosphere and roots of rice (Chang et al 2021) and tea plantations (Chen et al 2021). In addition, bacteria within the families Rhizobiaceae, Comamonadaceae, and Xanthobacteraceae have been closely linked to N cycling processes including N-fixation, nitrification, and denitrification in the past studies (Chen and Ni 2011;Gomez-Alvarez et al 2014;Jang et al 2020), which might help explain the soil N dynamics of the gravel pit.…”

Section: Discussionmentioning

confidence: 99%

Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance

Padda

Puri

Nguyen³

et al. 2022

Plant Soil

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Aims Despite little soil development and organic matter accumulation, lodgepole pine (Pinus contorta var. latifolia) consistently shows vigorous growth on bare gravel substrate of aggregate mining pits in parts of Canadian sub-boreal forests. This study aimed to investigate the bacterial microbiome of lodgepole pine trees growing at an unreclaimed gravel pit in central British Columbia and suggest their potential role in tree growth and survival following mining activity. Methods We characterized the diversity, taxonomic composition, and relative abundance of bacterial communities in rhizosphere and endosphere niches of pine trees regenerating at the gravel pit along with comparing them with a nearby undisturbed forested site using 16S rRNA high-throughput sequencing. Additionally, the soil and plant nutrient contents at both sites were also analyzed. Results Although soil N-content at the gravel pit was drastically lower than the forest site, pine tissue N-levels at both sites were identical. Beta-diversity was affected by site and niche-type, signifying that the diversity of bacterial communities harboured by pine trees was different between both sites and among various plant-niches. Bacterial alpha-diversity was comparable at both sites but differed significantly between belowground and aboveground plant-niches. In terms of composition, pine trees predominantly associated with taxa that appear plant-beneficial including phylotypes of Rhizobiaceae, Acetobacteraceae, and Beijerinckiaceae at the gravel pit and Xanthobacteraceae, Acetobacteraceae, Beijerinckiaceae and Acidobacteriaceae at the forest site. Conclusions Our results suggest that, following mining activity, regenerating pine trees recruit bacterial communities that could be plant-beneficial and support pine growth in an otherwise severely N-limited disturbed environment.

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“…For example, a recent study showed that self-cross of rice ( Oryza sp.) decreased the differences in rhizosphere bacterial and fungal communities between parental lines and progeny generations ( Chang et al, 2021 ). So, it is necessary to combine traditional plant cross-breeding with soil microbiomes ( Nerva et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

The structure and assembly of rhizobacterial communities are influenced by poplar genotype

Zhu

Yan²,

Wang³

et al. 2022

Front. Microbiol.

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The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3–-N content and 58 genera to NH4+-N/NO3–-N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3–-N content and fluctuated with increasing NH4+-N/NO3–-N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

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Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere

Cited by 10 publications

References 76 publications

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance

The structure and assembly of rhizobacterial communities are influenced by poplar genotype

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