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Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties.

ABSTRACT: Ribosomal 16S rRNA gene pyrosequencing was used to explore whether the genetically modified (GM) Bt-maize hybrid MON 89034 × MON 88017, expressing three insecticidal recombinant Cry proteins of Bacillus thuringiensis, would alter the rhizosphere bacterial community. Fine roots of field cultivated Bt-maize and three conventional maize varieties were analyzed together with coarse roots of the Bt-maize. A total of 547,000 sequences were obtained. Library coverage was 100% at the phylum and 99.8% at the genus rank. Although cluster analyses based on relative abundances indicated no differences at higher taxonomic ranks, genera abundances pointed to variety specific differences. Genera-based clustering depended solely on the 49 most dominant genera while the remaining 461 rare genera followed a different selection. A total of 91 genera responded significantly to the different root environments. As a benefit of pyrosequencing, 79 responsive genera were identified that might have been overlooked with conventional cloning sequencing approaches owing to their rareness. There was no indication of bacterial alterations in the rhizosphere of the Bt-maize beyond differences found between conventional varieties. B. thuringiensis-like phylotypes were present at low abundance (0.1% of Bacteria) suggesting possible occurrence of natural Cry proteins in the rhizospheres. Although some genera indicated potential phytopathogenic bacteria in the rhizosphere, their abundances were not significantly different between conventional varieties and Bt-maize. With an unprecedented sensitivity this study indicates that the rhizosphere bacterial community of a GM maize did not respond abnormally to the presence of three insecticidal proteins in the root tissue.

SUBMITTER: Dohrmann AB

PROVIDER: S-EPMC3526185 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties.

Dohrmann Anja B AB Küting Meike M Jünemann Sebastian S Jaenicke Sebastian S Schlüter Andreas A Tebbe Christoph C CC

The ISME journal 20120712 1

Ribosomal 16S rRNA gene pyrosequencing was used to explore whether the genetically modified (GM) Bt-maize hybrid MON 89034 × MON 88017, expressing three insecticidal recombinant Cry proteins of Bacillus thuringiensis, would alter the rhizosphere bacterial community. Fine roots of field cultivated Bt-maize and three conventional maize varieties were analyzed together with coarse roots of the Bt-maize. A total of 547,000 sequences were obtained. Library coverage was 100% at the phylum and 99.8% at ...[more]

PMID: 22791236

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Project description:BackgroundBacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear.ResultsWe quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content.ConclusionsIn conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.

Project description:This study was conducted to investigate the effect of biofertilizers on the structure and diversity of the rhizosphere bacterial community of maize. Different biofertilizers were applied to maize. The physical and chemical properties of rhizosphere soil samples were analyzed and the rhizosphere bacteria were analyzed by 16S amplicon sequencing. The results showed that treatment with Bacillus licheniformis and B. amyloliquefaciens as biofertilizers increased the soil organic matter (SOM), total nitrogen, total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents, indicating that the plant growth-promoting rhizobacteria in the biofertilizers might help the host plant to produce root exudates that, in return, recruit beneficial communities due to available sugars, amino acids, organic acids, vitamins, and polymers. The rhizosphere of maize treated with B. subtilis biofertilizer had the highest diversity and richness. However, the rhizosphere treated with the combined bacterial strains had the lowest diversity and richness, which might be due to the directional increase of the abundance of some bacteria with special functions, but the decrease of the overall bacterial community diversity in the soil. The dominant bacterial phyla were Proteobacteria (32.2%-34.6%), Acidobacteria (15.0%-21.0%), Actinobacteria (13.1%-17.2%), and Gemmatimonadetes (9.0%-10.8%), and the dominant bacterial species were Aciditerrimonas ferrireducens JCM 15389 (4.3%-5.2%), Gemmatimonas aurantiaca (3.2%-4.1%), and Pyrinomonas methylaliphatogenes (2.1%-4.8%). The significantly enriched bacterial functions were associated with amino acid metabolism, sugar metabolism, and energy metabolism pathways. The results of a redundancy analysis showed that SOM, TP, and AK were the main factors affecting the microbial community structure in the maize rhizosphere. In conclusion, the application of biofertilizers increased the diversity and richness of the bacterial community in the maize rhizosphere soil. However, combined strain treatment was failed and not an ideal strategy due to the lowest abundance and diversity.

Project description:Microbes, especially abundant microbes in bulk soils, form multiple ecosystem functions, which is relatively well studied. However, the role of rhizosphere microbes, especially rhizosphere rare taxa vs. rhizosphere abundant taxa in regulating the element circling, multifunctionality, aboveground net primary productivity (ANPP) and the trade-offs of multiple functions remains largely unknown. Here, we compared the multiple ecosystem functions, the structure and function of rhizosphere soil bacterial and fungal subcommunities (locally rare, locally abundant, regionally rare, regionally abundant, and entire), and the role of subcommunities in the Zea mays and Sophora davidii sole and Z. mays/S. davidii intercropping ecosystems in subtropical China. Results showed that intercropping altered multiple ecosystem functions individually and simultaneously. Intercropped Z. mays significantly decreased the trade-off intensity compared to sole Z. mays, the trade-off intensity under intercropped S. davidii was significantly higher than under intercropped Z. mays. The beta diversities of bacterial and fungal communities, and fungal functions in each subcommunity significantly differed among groups. Network analysis showed intercropping increased the complexity and positive links of rare bacteria in Z. mays rhizosphere, but decreased the complexity and positive links of rare bacteria in S. davidii rhizosphere and the complexity and positive links of fungi in both intercropped plants rhizosphere. Mantel test showed significant changes in species of locally rare bacteria were most strongly related to nitrogen-cycling multifunctionality, ANPP and trade-offs intensity, significant changes in species of locally rare fungus were most strongly related to carbon-cycling multifunctionality, phosphorus-cycling multifunctionality, and average ecosystem multifunctionality. This research highlights the potential and role of rare rhizosphere microorganisms in predicting and regulating system functions, productivity, and trade-offs.

Project description:Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage. IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.

Dataset Information

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties.

Publications

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties.

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