Environmental Microbiome
Investigate Environmental Quality and Productivity with Advanced Microbial Insights
Leverage Cosmos-Hub for comprehensive soil and water microbiome analysis in studies from crop yields to water health.
Why Soil, Water, and Air Matters
Microbes in soil and water are foundational to both agricultural productivity and environmental sustainability. Healthy soil microbiomes enrich crop yields and biodiversity, while clean water ensures the health of aquatic life and the broader ecosystem. CosmosID-HUB facilitates the integration of microbial insights from these resources, enabling better management and conservation practices. By understanding and improving the microbial health of soil and water, researchers can significantly impact food security, water quality, and ecological diversity.
Applications in Soil and Water Microbiology
Cosmos-Hub’s advanced tools provide crucial insights into the microbiomes of both soil and water. This analysis is essential for:
- Enhancing agricultural yields through optimized soil health.
- Improving water quality management for conservation and regulatory compliance.
- Studying the interplay between soil and water ecosystems to develop integrated management strategies that support sustainability.


Sample Types in Environmental Microbiome Research
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Soil Samples
- Topsoil: Surface layer, rich in organic matter and microbes.
- Subsoil: Deeper layers, with nutrient and moisture variations.
- Rhizosphere: Near plant roots, key for plant-microbe studies.
- Bulk Soil: Provides a baseline of the microbial community away from plant influence.
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Sediment Samples
- River Sediments: Collect from riverbeds, important for studying waterborne microbial communities and pollutant impacts.
- Lake Sediments: Often collected at various depths, useful for understanding sedimentation and historical microbial activity.
- Oceanic Sediments: Taken from sea floors, crucial for studying deep-sea ecosystems and biogeochemical cycles.
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Water Samples
- Freshwater: From rivers, lakes, and streams, focusing on microbial diversity and water quality.
- Brackish Water: From estuaries, where fresh and saltwater mix, important for studying transition zone ecosystems.
- Marine Water: From oceans, critical for global biogeochemical processes and marine microbiology.
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Core Samples
- Soil Cores: Vertical profiles of soil layers.
- Ice Cores: From glaciers and ice caps, capturing long-term climate data and ancient microbes.
- Sediment Cores: From aquatic beds, providing historical microbial and environmental data.
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Seasonal and Temporal Samples
Periodic Sampling: Collecting samples across seasons or over years to observe changes due to environmental or anthropogenic factors.
How Cosmos-Hub Helps
Quick and accurate processing of sequencing data to uncover bacterial and fungal profiles from samples.
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Advanced statistics tools like MaAsLin for longitudinal and complex study data.
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Advanced statistics tools like MaAsLin for longitudinal and complex study data.
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KEPLER's host-agnostic profiling makes it ideal for studying microbiomes across diverse soil and water types species.
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Publications and Success Stories
Real-World Impact of Soil Microbiome Analysis with Cosmos-Hub
- Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year
Hassard, F., Vu, M., Rahimzadeh, S., Castro-Gutierrez, V., Stanton, I., Burczynska, B., Wildeboer, D., Baio, G., Brown, M. R., Garelick, H., Hofman, J., Kasprzyk-Hordern, B., & Grimsley, J. (2023). PLOS ONE, 18(5), e0286259.
https://doi.org/10.1371/journal.pone.0286259 - Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land
Ibekwe, A. M., Bhattacharjee, A. S., Phan, D., Ashworth, D., Schmidt, M. P., Murinda, S. E., Obayiuwana, A., Murry, M. A., Schwartz, G., Lundquist, T., Ma, J., Karathia, H., Fanelli, B., Hasan, N. A., & Yang, C.-H. (2023). Science of The Total Environment, 872, 162194.
https://doi.org/10.1016/j.scitotenv.2023.162194 - Water microbiota from a commercial alfalfa sprout crop over 4 days of growth
Reed, E., Sanderson, R., Sanderson, B., Ramachandran, P., Commichaux, S., Brown, E., Zheng, J., Strain, E., & Ottesen, A. (2021). Microbiology Resource Announcements, 10(2), e00906-20.
https://doi.org/10.1128/MRA.00906-20 - A comparative analysis of drinking water employing metagenomics
Brumfield, K. D., Hasan, N. A., Leddy, M. B., Cotruvo, J. A., Rashed, S. M., Colwell, R. R., & Huq, A. (2020). PLOS ONE, 15(4), e0231210.
https://doi.org/10.1371/journal.pone.0231210 - Characterization of the microbiome at the world's largest potable water reuse facility
Stamps, B. W., Leddy, M. B., Plumlee, M. H., Hasan, N. A., Colwell, R. R., & Spear, J. R. (2018). Frontiers in Microbiology, 9, 2435.
https://doi.org/10.3389/fmicb.2018.02435 - Characterization of the microbiota of oyster larvae (Crassostrea virginica) and tank water from an aquaculture system with high and low larval survival rates
Ramachandran, P., Reed, E., Commichaux, S., Strain, E., DePaola, A., Rikard, S., & Ottesen, A. (2018). Genome Announcements, 6(25), e00597-18.
https://doi.org/10.1128/genomeA.00597-18 - Effect of disinfectant, water age, and pipe materials on bacterial and eukaryotic community structure in drinking water biofilm
Wang, H., Masters, S., Edwards, M. A., Falkinham, J. O., & Pruden, A. (2014). Environmental Science & Technology, 48(3), 1426–1435.
https://doi.org/10.1021/es402636u
Ready to Advance Your Soil Microbiome Research?
Unlock the power of high-resolution microbiome analysis with Cosmos-Hub.