Multi-Omics Approach To Studying The Impacts Of Cover Crops On Soil-Plant-Microbiome Interactions In Crop Production Systems

Cover crops are increasingly adopted as a tool for improving soil health in US agriculture. Growers are demanding cover crops that serve a broader range of cropping systems, and a better understanding of how to deploy them for the greatest soil health benefit. Through this Research Topic, we aim to provide accurate information about how the effect of cover crops will impact soil health in the agricultural landscape. As the benefits mediated by shifts in the soil microbiome are not yet understood enough to be incorporated into current cash crop recommendations, we aim to make a strong move toward correcting that knowledge deficit.

It is imperative to address this by connecting genomic characterization of the soil microbiome with soil functional responses that can be applied at the field level, to fine-tune cover crops as a soil health-promoting practice for crop production systems. The cover crops differ markedly in their functional impacts belowground, which allows us to test mechanisms of soil-health promotion that are mediated by cover crops and identify those specific to different field crops. When considering how to interpret data describing soil microbial communities, the impacts of recent methodological advances for identifying the full range of microbiota in environmental samples cannot be overstated.

Historically, microbial components of ecosystems were largely treated as an unknown mix of organisms – the ‘black box’ of microbial ecology. More sophisticated approaches such as analyses of full soil metagenomes using shotgun or long-read DNA sequencing and community interaction networks help address this challenge. They provide information not just on taxonomic diversity, but also on functional gene diversity and community-level traits. This Research Topic will also promote multi-omics approaches such as transcriptomics, metagenomics, proteomics, and metabolomics to study soil-plant-covercrop-microbiome interactions.

This Research Topic aims to elucidate the complex interactions between cover crops, soil health, and the soil microbiome using a multi-omics approach. By integrating genomic, transcriptomic, proteomic, and metabolomic data, we seek to uncover the mechanisms by which cover crops influence soil microbial communities and, in turn, how these communities affect soil health and crop productivity. Specific questions include: How do different cover crops alter the soil microbiome? What are the functional consequences of these changes for soil health and crop yield? Can we identify specific microbial taxa or genes that are key indicators of soil health?

To gather further insights into the impacts of cover crops on soil-plant-microbiome interactions, we welcome articles addressing, but not limited to, the following themes:
- Comparative analysis of soil microbial communities under different cover crop regimes
- Functional gene diversity and its role in soil health
- Metagenomic and metatranscriptomic profiling of soil microbiomes
- Impact of cover crops on soil nutrient cycling and plant health
- Interaction networks within soil microbial communities
- Use of proteomics and metabolomics to understand soil-plant-microbiome interactions
- Evaluation of biocontrol agents and their role in promoting soil and plant health
- Long-term field studies on the impact of cover crops on soil health and crop productivity

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Policy Brief
• Review
• Systematic Review

Keywords: Soil microbiome, plant microbiome, plant-microbiome interactions, metagenomics, cover crop- microbiome, agroecology, multi-omics

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.