This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Qiang Zhuge
Nanjing Forestry University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Poplar (Populus) is a genus of globally important plantation trees used widely in industrial and agricultural production. However, poplar is easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in a decline in poplar quality. Due to their strong insect resistance, Bt toxin-encoded Cry genes have been widely adopted in poplar breeding; however, potential adverse effects of Cry1Ah1-modified poplars on the ecological environment have raised concerns.
Results: In this study, we comprehensively analyzed the structural and functional composition of the rhizosphere microbiome in field-grown transgenic Bt poplar.
Conclusions: Our analysis of soil chemistry patterns revealed that soil alkaline nitrogen, soil available phosphorus, and microbial biomass nitrogen and phosphorus levels were improved, whereas microbial biomass carbon declined in Cry1Ah1-modified poplar rhizosphere samples. We applied metagenomic sequencing of Non-Transgenic (NT) and Cry1Ah1-modified poplar rhizosphere samples collected from a natural field; the predominant taxa included Proteobacteria, Acidobacteria, and Actinobacteria. We also identified microbial functional traits involved in membrane transport, amino acid metabolism, carbohydrate metabolism, and replication and repair in NT and Cry1Ah1-modified poplars. Together, these results demonstrate that the NT and Cry1Ah1-modified poplar rhizosphere microbiomes had similar diversity and structure. These differences in relative abundance were observed in a few genera but did not affect the primary genera or soil.
Keywords
Bt toxins, Cry1Ah1-modified poplar, metagenomic sequencing, poplar, rhizosphere
Figure 1
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Figure 3
Figure 4
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Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- supplementalfigure1.jpg
Supplemental Figure 1 Analysis of the taxonomic distinctiveness of poplar rhizosphere soil bacteria based on alpha diversity. (A) Chao1 index. (B) Observed species index. (C) Phylogenetic diversity whole-tree index. (D) Shannon index.
- supplementalfigure1.jpg
Supplemental Figure 1 Analysis of the taxonomic distinctiveness of poplar rhizosphere soil bacteria based on alpha diversity. (A) Chao1 index. (B) Observed species index. (C) Phylogenetic diversity whole-tree index. (D) Shannon index.
- supplementalfigure2.jpg
Supplemental Figure 2 Taxonomic analysis of bacteria distribution at class (A), order (B), genus (C), and species (D) levels between rhizosphere samples from the Cry1Ah1-modified and non-transgenic (NT) varieties based on 16S amplicon and metagenomic data.
- supplementalfigure2.jpg
Supplemental Figure 2 Taxonomic analysis of bacteria distribution at class (A), order (B), genus (C), and species (D) levels between rhizosphere samples from the Cry1Ah1-modified and non-transgenic (NT) varieties based on 16S amplicon and metagenomic data.
- supplementalfigure3.jpg
Supplemental Figure 3 Relative abundances of fungi at the phylum level between NT and Cry1Ah1-modified varieties. (A) Rare operational taxonomic unit (OTU) data were used to visualize the distribution of all 18 phyla in a heatmap of relative abundances. (B) Significance tests of fungi high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure3.jpg
Supplemental Figure 3 Relative abundances of fungi at the phylum level between NT and Cry1Ah1-modified varieties. (A) Rare operational taxonomic unit (OTU) data were used to visualize the distribution of all 18 phyla in a heatmap of relative abundances. (B) Significance tests of fungi high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure4.jpg
Supplemental Figure 4 Relative abundances of fungi at the genus level between NT and Cry1Ah1-modified varieties. (A) Rare OTU data were used to visualize the distribution of all 19 genera in a heatmap of relative abundances. (B) Significance tests of fungi with high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way ANOVA and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure4.jpg
Supplemental Figure 4 Relative abundances of fungi at the genus level between NT and Cry1Ah1-modified varieties. (A) Rare OTU data were used to visualize the distribution of all 19 genera in a heatmap of relative abundances. (B) Significance tests of fungi with high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way ANOVA and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure5.jpg
Supplemental Figure 5 Kyoto Encyclopedia of Genes and Genomes level 2 pathway functional comparison of rhizosphere soil fungi from the NT and Cry1Ah1-modified varieties.
- supplementalfigure5.jpg
Supplemental Figure 5 Kyoto Encyclopedia of Genes and Genomes level 2 pathway functional comparison of rhizosphere soil fungi from the NT and Cry1Ah1-modified varieties.
- supplementalfigure6.jpg
Supplemental Figure 6 Analysis of bacterial community structure and composition related to nitrogen and phosphorus metabolism between NT and Cry1Ah1-modified varieties. Relative abundance of Bradyrhizobium (A), Frankia (B), Nitrosospira (C), Pseudomonas (D), Rhizobium (E), Bacillus (F), Streptomyces (G), Flavobacterium (H), Paenibacillus (I), Pseudarthrobacter (J), and Serratia (K) at the genus level between NT and Cry1Ah1-modified varieties.
- supplementalfigure6.jpg
Supplemental Figure 6 Analysis of bacterial community structure and composition related to nitrogen and phosphorus metabolism between NT and Cry1Ah1-modified varieties. Relative abundance of Bradyrhizobium (A), Frankia (B), Nitrosospira (C), Pseudomonas (D), Rhizobium (E), Bacillus (F), Streptomyces (G), Flavobacterium (H), Paenibacillus (I), Pseudarthrobacter (J), and Serratia (K) at the genus level between NT and Cry1Ah1-modified varieties.
- supplementaltable1.xlsx
Supplemental Table 1 The 16S rDNA tags and ITS1 tags generated from the rhizosphere microbiome.
- supplementaltable1.xlsx
Supplemental Table 1 The 16S rDNA tags and ITS1 tags generated from the rhizosphere microbiome.
- supplementaltable2.xlsx
Supplemental Table 2 OTUs for bacterial and fungal community sequencing.
- supplementaltable2.xlsx
Supplemental Table 2 OTUs for bacterial and fungal community sequencing.
- supplementaltable3.xlsx
Supplemental Table 3 Relative abundance of fungi at the phylum level between NT and Cry1Ah1-modified varieties.
- supplementaltable3.xlsx
Supplemental Table 3 Relative abundance of fungi at the phylum level between NT and Cry1Ah1-modified varieties.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Qiang Zhuge
Nanjing Forestry University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 23 Sep, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Poplar (Populus) is a genus of globally important plantation trees used widely in industrial and agricultural production. However, poplar is easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in a decline in poplar quality. Due to their strong insect resistance, Bt toxin-encoded Cry genes have been widely adopted in poplar breeding; however, potential adverse effects of Cry1Ah1-modified poplars on the ecological environment have raised concerns.
Results: In this study, we comprehensively analyzed the structural and functional composition of the rhizosphere microbiome in field-grown transgenic Bt poplar.
Conclusions: Our analysis of soil chemistry patterns revealed that soil alkaline nitrogen, soil available phosphorus, and microbial biomass nitrogen and phosphorus levels were improved, whereas microbial biomass carbon declined in Cry1Ah1-modified poplar rhizosphere samples. We applied metagenomic sequencing of Non-Transgenic (NT) and Cry1Ah1-modified poplar rhizosphere samples collected from a natural field; the predominant taxa included Proteobacteria, Acidobacteria, and Actinobacteria. We also identified microbial functional traits involved in membrane transport, amino acid metabolism, carbohydrate metabolism, and replication and repair in NT and Cry1Ah1-modified poplars. Together, these results demonstrate that the NT and Cry1Ah1-modified poplar rhizosphere microbiomes had similar diversity and structure. These differences in relative abundance were observed in a few genera but did not affect the primary genera or soil.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- supplementalfigure1.jpg
Supplemental Figure 1 Analysis of the taxonomic distinctiveness of poplar rhizosphere soil bacteria based on alpha diversity. (A) Chao1 index. (B) Observed species index. (C) Phylogenetic diversity whole-tree index. (D) Shannon index.
- supplementalfigure1.jpg
Supplemental Figure 1 Analysis of the taxonomic distinctiveness of poplar rhizosphere soil bacteria based on alpha diversity. (A) Chao1 index. (B) Observed species index. (C) Phylogenetic diversity whole-tree index. (D) Shannon index.
- supplementalfigure2.jpg
Supplemental Figure 2 Taxonomic analysis of bacteria distribution at class (A), order (B), genus (C), and species (D) levels between rhizosphere samples from the Cry1Ah1-modified and non-transgenic (NT) varieties based on 16S amplicon and metagenomic data.
- supplementalfigure2.jpg
Supplemental Figure 2 Taxonomic analysis of bacteria distribution at class (A), order (B), genus (C), and species (D) levels between rhizosphere samples from the Cry1Ah1-modified and non-transgenic (NT) varieties based on 16S amplicon and metagenomic data.
- supplementalfigure3.jpg
Supplemental Figure 3 Relative abundances of fungi at the phylum level between NT and Cry1Ah1-modified varieties. (A) Rare operational taxonomic unit (OTU) data were used to visualize the distribution of all 18 phyla in a heatmap of relative abundances. (B) Significance tests of fungi high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure3.jpg
Supplemental Figure 3 Relative abundances of fungi at the phylum level between NT and Cry1Ah1-modified varieties. (A) Rare operational taxonomic unit (OTU) data were used to visualize the distribution of all 18 phyla in a heatmap of relative abundances. (B) Significance tests of fungi high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure4.jpg
Supplemental Figure 4 Relative abundances of fungi at the genus level between NT and Cry1Ah1-modified varieties. (A) Rare OTU data were used to visualize the distribution of all 19 genera in a heatmap of relative abundances. (B) Significance tests of fungi with high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way ANOVA and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure4.jpg
Supplemental Figure 4 Relative abundances of fungi at the genus level between NT and Cry1Ah1-modified varieties. (A) Rare OTU data were used to visualize the distribution of all 19 genera in a heatmap of relative abundances. (B) Significance tests of fungi with high and low relative abundances between NT and Cry1Ah1-modified varieties. Data were analyzed using one-way ANOVA and Tukey’s post hoc comparison. *P < 0.05.
- supplementalfigure5.jpg
Supplemental Figure 5 Kyoto Encyclopedia of Genes and Genomes level 2 pathway functional comparison of rhizosphere soil fungi from the NT and Cry1Ah1-modified varieties.
- supplementalfigure5.jpg
Supplemental Figure 5 Kyoto Encyclopedia of Genes and Genomes level 2 pathway functional comparison of rhizosphere soil fungi from the NT and Cry1Ah1-modified varieties.
- supplementalfigure6.jpg
Supplemental Figure 6 Analysis of bacterial community structure and composition related to nitrogen and phosphorus metabolism between NT and Cry1Ah1-modified varieties. Relative abundance of Bradyrhizobium (A), Frankia (B), Nitrosospira (C), Pseudomonas (D), Rhizobium (E), Bacillus (F), Streptomyces (G), Flavobacterium (H), Paenibacillus (I), Pseudarthrobacter (J), and Serratia (K) at the genus level between NT and Cry1Ah1-modified varieties.
- supplementalfigure6.jpg
Supplemental Figure 6 Analysis of bacterial community structure and composition related to nitrogen and phosphorus metabolism between NT and Cry1Ah1-modified varieties. Relative abundance of Bradyrhizobium (A), Frankia (B), Nitrosospira (C), Pseudomonas (D), Rhizobium (E), Bacillus (F), Streptomyces (G), Flavobacterium (H), Paenibacillus (I), Pseudarthrobacter (J), and Serratia (K) at the genus level between NT and Cry1Ah1-modified varieties.
- supplementaltable1.xlsx
Supplemental Table 1 The 16S rDNA tags and ITS1 tags generated from the rhizosphere microbiome.
- supplementaltable1.xlsx
Supplemental Table 1 The 16S rDNA tags and ITS1 tags generated from the rhizosphere microbiome.
- supplementaltable2.xlsx
Supplemental Table 2 OTUs for bacterial and fungal community sequencing.
- supplementaltable2.xlsx
Supplemental Table 2 OTUs for bacterial and fungal community sequencing.
- supplementaltable3.xlsx
Supplemental Table 3 Relative abundance of fungi at the phylum level between NT and Cry1Ah1-modified varieties.
- supplementaltable3.xlsx
Supplemental Table 3 Relative abundance of fungi at the phylum level between NT and Cry1Ah1-modified varieties.
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