Soil & Rhizosphere Microbiome Analysis
Discover the Hidden Microbial Networks That Drive Soil Health
Accelerate agricultural innovation and environmental stewardship with Cosmos-Hub's comprehensive soil and rhizosphere microbiome insights.
Why Soil & Rhizosphere Microbiome Analysis Matters
Soil microbes are the unsung heroes of global agriculture, driving nutrient cycles, carbon storage, and plant performance. The rhizosphere—the soil region closely surrounding plant roots—is where the most intense biological interactions occur. Analyzing this zone can unlock powerful insights into plant-microbe symbiosis, disease resistance, and sustainable crop yields.
With increasing demand for regenerative practices, data-driven soil microbiome analysis offers growers and researchers a blueprint for healthier soils and more resilient crops.
Example Sample Types for Soil & Rhizosphere Microbiome Studies
- Agricultural soil before and after treatment
- Rhizosphere samples collected at different crop growth stages
- Organic vs conventional field comparisons
- Vineyard, orchard, and greenhouse soil substrates
- Soil from reforestation or cover crop trials
- Compost-amended soils
- Drought - and nutrient-stressed root zones
How Cosmos-Hub Powers Soil & Rhizosphere Microbiome Discovery
Tailored workflows for soil and rhizosphere sequencing datasets
Functional and taxonomic profiling for nitrogen fixation, phosphorus solubilization, and stress-resilient communities
Longitudinal tracking of microbial shifts due to irrigation, fertilizer, or crop rotation strategies
Granular analytics to differentiate root-associated microbiota from bulk soil signals
Relevant Pipelines
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Kepler™: Host-Agnostic Taxonomic & Functional Profiling
Kepler™ offers a robust, reference-free engine for functional annotation, enabling deep insights into soil microbe activity and ecosystem services.
Cosmos-Hub offers Kepler™ in combination with a host-agnostic functional pipeline, Functional 2.0, which interrogates shotgun metagenomic and metatranscriptomic data to understand metabolic and biochemical potential by annotating translated reads with numerous functional databases:
- MetaCyc Pathways,
- Enzyme Commissions,
- Pfam,
- CAZy,
- GO Terms.
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Emu: Long-Read Amplicon Profiling
Emu is a growingly popular tool designed specifically for long-read amplicon data generated by Oxford Nanopore Technologies or Pacific Biosciences instrumentation. The Cosmos-Hub iteration of Emu is built with flexibility in mind, allowing users to analyze 16S, ITS, 18S or full 16S-18S-23S full operon data. Additionally, many databases have been implemented to allow users to tailor their analysis to their sample type and study questions:- 16S Amplicon: GreenGenes2, SILVA, GreenGenes2, GTDB SSU 220, EMU Default, MIDAS, HOMDB.
- ITS Amplicon: UNITE
- 18S Amplicon: SILVA
- 16S-ITS-23S Full Operon: RRN
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Short-Read Amplicon Profiling
Our amplicon sequencing workflows provide high-resolution taxonomic profiling of microbial communities using targeted regions—16S rRNA for bacteria and archaea, and ITS for fungi.
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The short-read 16S pipeline utilizes the DADA2 algorithm for denoising and ASV inference, ensuring genus resolution of bacterial taxa. Taxonomy is assigned using the SILVA database, and community-level functional potential via Metacyc Pathways and Enzyme Commissions is inferred with PICRUSt2.
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The short-read ITS pipeline is optimized for fungal community profiling, leveraging the QIIME framework along with the UNITE database for closed-reference OTU picking. It processes reads through trimming and merging, outputting tables of OTU IDs, frequencies, and relative abundances.
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Ready to Cultivate a Deeper Understanding of Soil Health?
Unlock the power of high-resolution microbiome analysis with Cosmos-Hub.
Frequently Asked Questions
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Can Cosmos-Hub handle high-complexity soil samples?
Yes. Cosmos-Hub is optimized for the diversity and density of soil metagenomes, delivering accurate results across carious soil types.
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Does it support functional as well as taxonomic profiling?
Absolutely. Functional modules identify genes linked to nutrient cycling, resistance traits, and more.
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How are rhizosphere samples processed differently?
The platform accommodates root-adhered soil and can distinguish it from bulk soil microbial communities for high-resolution insights.
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Can I compare microbial communities across sites and conditions?
Yes. Cosmos-Hub supports robust cohort analyses and metadata-driven comparisons. -
What kind of output can I expect?
Interactive visualizations, downloadable tables, and publication-ready graphics tailored for environmental microbiome research.