Bacterial community structure in soils of the oldest agronomic experiment fields in the united states, the morrow plots, and of the original tallgrass prairie
Date
2019-05
Authors
Ganesan, Abiramasundari
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Abstract
Diversity of soil microbial communities and their influence on plants growth are widely studied to develop and improve sustainable agricultural practices. Soil-microbe interactions are very complex to interpret given that it involves other biotic and abiotic environmental factors, and the traditional culture-based methods followed by physicochemical analysis are either extremely laborious or not robust enough to investigate the broad picture and intricate details of these complex interactions. The use of molecular technologies like qPCR has resolved some of the shortcomings of culture-based methods, but still exhibited biases in both qualitative and quantitative analyses of microbial communities. New molecular techniques that focus on high throughput DNA sequencing techniques such as 454 pyrosequencing and the MiSeq sequencing platforms revolutionized the field of microbial diversity studies. These techniques are widely used in projects such as the Earth Microbiome Project (EMP), a collective attempt to establish microbial fingerprints in different environments of the planet. Additional applications include studies on long-term effects of crop rotation and different fertilization regimen on bacterial community structure. We tried to build on these studies and assess microbial community structure in the Morrow Plots, the oldest agronomic experimental fields in the United States, and adjacent tallgrass prairie with emphasis on members of the genus Frankia. The Morrow Plots were established in 1876 on tallgrass prairie soils to evaluate the effects of different cropping systems and soil treatments on crop yields, and include the oldest continuous corn plots in the world. Illumina-based 16S rRNA V3 gene amplicon sequencing retrieved a total of 26.47 M effective sequences obtained from 44 samples, i.e. 12 soils with different vegetation and fertilization regimen, and 3 to 6 replicates per soil, with 313,695 to 906,328 reads per sample. At a sequencing depth of 300,000 sequences for each sample, Acidobacteria, Actinobacteria, Proteobacteria and Verrumicrobia were the most abundant bacterial phyla present across all soil samples accounting for 74±4% of the reads. Crop rotation increased diversity of the bacterial community, which was also affected by the fertilization regimen. Reads representing frankiae accounted for 0.1 to 1.0% of all reads, with generally higher percentages in fertilized soils. Reads represented frankiae of clusters 1a, 2, 3, and 4, but also a group of frankiae that could not reliably be assigned to a cultured relative. The results provide evidence of long-term establishment of Frankia populations in agricultural soils under different management conditions.
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Keywords
Next-generation sequencing, 16S rRNA
Citation
Ganesan, A. (2019). Bacterial community structure in soils of the oldest agronomic experiment fields in the united states, the morrow plots, and of the original tallgrass prairie (Unpublished thesis). Texas State University, San Marcos, Texas.