Profiling Microbial Communities in Soils from Organic, Sustainable, and Conventional Cropping Systems

View the project final report

• 2012 annual report

Commodities

• Agronomic: general grain crops

Practices

• Crop Production: crop rotation, organic fertilizers
• Education and Training: on-farm/ranch research
• Production Systems: organic agriculture
• Soil Management: soil analysis, soil microbiology

This project investigated the effects of long-term organic and conventional management on bacterial community structures in agricultural soils using 16S metagenomic sequencing. Due to the cost of sequencing at the time the experiment was designed, we were not able to use sufficient replication to overcome the enormous variability arising from the heterogeneity of the soil environment, so we did not detect differences in structure or diversity due to management, crop, or sampling site. Bacterial community structure did differ by sampling site, suggesting that soil type plays a greater role in structuring bacterial communities than management system or crop. However, we generated 22 detailed phylogenetic profiles of agricultural soil bacterial communities. We also used the information obtained in this experiment about expected variability in 16S profiles in the design of a follow-up experiment (currently in progress) that investigates the effects of cover crops and organic fertilizers on soil microbial community structure and function.

Introduction:

The impact of agricultural practices, particularly organic farming, on soil biological properties has long been a subject of interest, but only in the last few years have researchers begun to use molecular techniques to investigate the impact of agricultural practices on soil microbial communities. These techniques enable investigation of entire communities, including those microbes that cannot be grown in culture, which constitute the large majority of soil populations. Recent developments in high-throughput next-generations sequencing have allowed whole-community, or metagenomic, DNA sequencing. This project uses metagenomic 16S sequencing to investigate the structure and diversity of soil bacterial communities under long-term organic and conventional management. To our knowledge, this is the first study to date using 16S sequencing in organic field crop systems.

The stated objective of this project were 1) to construct a set of phylogenetic profiles of soil communities under a broad range of management practices, which will allow us to determine which bacterial populations are favored by which practices, and 2) to use these profiles to make predictions about the metabolic capabilities of these communities, which can be used to guide further research into the impacts of organic and conventional practices on soil biological functions.

This project did achieve the objective of generating multiple snapshot-style profiles of soil bacterial communities across a wide range of soil types and agronomic practices. Because we were not able to detect differences in microbial community structure associated with management system or crop, we were not able to use our phylogenetic profiles to predict differences in soil microbial function.

Since this project was initiated, the cost of metagenomic sequencing has dropped dramatically, allowing us to design a follow-up experiment that makes use of replication and subsampling to address the diversity and heterogeneity of soil communities. The follow-up experiment, which was initiated in 2011, investigates the relationship between soil microbial community structure and metabolic function in a much more explicit and statistically rigorous manner than was possible within the constraints of the original experiment.