Fungal Pathogen Detection for Crop Rotation Planning
Screen soil, roots, plants, or seed for validated pathogenic fungi-plus a full fungal profile-so growers, advisors, and product teams can assess disease risk and field–crop fit before next season.
UNIVERSITYHospital of Aarhus
University of AarhusSEGESInnovationUNIVERSITYHospital of AarhusUniversity of AarhusSEGESInnovationReduce rotation risk
Know whether key soil-borne fungi pathogens are present-and at what level-before choosing the next crop or variety.
Target actions, not guesswork
Use quantified pathogen signals plus the full fungal context to support practical decisions (rotation, hygiene, inputs, seed choices).
Built for field decisions
Clear presence/absence + level reporting for validated targets, combined with a broad fungal overview for a complete picture.
Why single-pathogen tests leave you exposed
Most soil checks are single-pathogen, symptom-driven, or based on field history. That means you can miss silent build-up - and you don't get a comparable view across the full disease threat profile.
Biomcare's Fungi Load Test screens multiple key soil-borne fungal pathogens in one assay, plus a broad fungal profile for context.
You get one test that helps predict next-season fungal disease risk - so you can plan crop rotation, variety, and protection strategy before you commit seed, inputs, and budget.
What a fungi analysis helps you do
- Reduce yield risk by seeing which fungi are actually present
- Match crop choice and genetics to real disease pressure
- Target fungicide strategy and timing to the threat profile
- Prioritize actions using data - not guesswork
- Build rotations that break fungal cycles and lower future pressure
“We have had the pleasure of working with Biomcare for the past four years on a variety of soil research projects, gaining new insights into the complexity of the soil microbiome ... we have been highly satisfied with the quality of service.”
Sidsel Birkelund Schmidt
Special Consultant, PhD in Plant Nutrition, cand.agro
Innovation Center for Organic Farming
Who this is for
Farmers / growers
You need a clearer basis for choosing next season's crop and reducing avoidable disease losses-especially where rotation options are tight.
Advisors and trial/monitoring programmes
You need consistent, comparable fungal data across fields or clients to guide recommendations and document risk.
Manufacturers and product teams (seed, treatments, biologicals)
You need pre-season fungal pressure data to support positioning, guidance, and targeted trials-without relying only on visible symptoms.
What the test delivers
Validated pathogen panel (9 targets)
You receive presence/absence and level for nine validated pathogenic fungi. Unlike single-target tests that screen for one pathogen at a time, this panel captures multiple validated risks in one structured analysis-providing a broader and more comparable disease picture from the same sample.
Broad fungal profile (full context)
You receive an overview of the overall fungal community (beneficial, potentially harmful, saprotrophs, and unknowns) to understand diversity and dominance patterns-not just single pathogens. This added context helps interpret whether risk is isolated or part of a broader imbalance-supporting more precise rotation and management decisions.
Validated pathogens
| Validated pathogen | Typical disease | Examples of crops impacted |
|---|---|---|
| Ascochyta fabae | Horse bean leaf spot | Horse bean |
| Ascochyta pisi var. pisi (Didymella pisi) | Ascochyta blight (pea) | Pea |
| Berkeleyomyces basicola | Black root rot | Horse bean, pea, strawberry, raspberry, carrot, cucurbits (incl. cucumber, melon, watermelon) |
| Botrytis fabae / Botrytis cinerea | Chocolate spot (fabae), grey mould (cinerea), chocolate spot | Oilseed rape, Horse bean, pea, grapevine, strawberry, tomato, cucumber, lettuce |
| Fusarium avenaceum | Root/foot rot; in cereals part of head blight complex | Oilseed rape, maize, Horse bean, pea, cereals, potato, carrot, strawberry |
| Fusarium oxysporum | Wilt disease; root rot complex | Horse bean, pea, onion, tomato, potato, spinach |
| Rhizoctonia solani | Damping-off / root rot / stem base rot; in potato black scurf | Oilseed rape, maize, pea, soybean, rice, potato, tomato, vegetables |
| Sclerotinia sclerotiorum | Stem rot / white mould | Oilseed rape, Horse bean, pea, potato, carrot, soybean, sunflower, blackcurrant, strawberry |
| Verticillium longisporum | Verticillium wilt (oilseed rape/cabbage family) | Oilseed rape, cabbage, broccoli, cauliflower, mustard |
Note: For Botrytis fabae and B. cinerea, the test reports the presence of one or both (they are not separated at species level in the validated readout).
How it works
Order, collect & ship
Contact us to get started - we'll send you a sample sheet and shipping instructions. For soil, collect 8–16 cores across the field, mix in a clean bucket, and transfer ~3–4 ml into a labeled container. [Step-by-step guide →]
We analyse your sample
We process soil, root, plant, and seed samples using sequencing-based workflows - combining broad fungal detection with quantification to give results at meaningful levels.
You get an actionable report
Validated pathogen results first, broad fungal context second - with clear interpretation guidance built for practical decision-making.
What you get
Validated pathogen results (decision layer)
Presence/absence for the 9 validated targets Level and relative contribution (so you can see whether a pathogen is a trace signal or a dominant pressure)
Broad fungal profile (context layer)
Top fungal taxa with role category (beneficial / potential pathogen / saprotroph / unclear) Diversity and dominance context to support interpretation beyond single targets
Practical interpretation framework
A consistent way to read results that considers both relative share and overall fungal load, to avoid overreacting to small signals when total fungal load is low.
Interpretation support (optional review call)
A structured results walkthrough with a Biomcare specialist-so you can ask questions, challenge assumptions, and understand exactly what is behind the numbers.
How our clients use this service
Pre-season screening of fields to decide whether peas/faba beans are a good fit next year
Identifying elevated Sclerotinia or Verticillium risk before planning oilseed rape rotation
Checking pathogen pressure in greenhouse or high-value cropping systems where losses are costly
Comparing multiple fields/farms in an advisory programme to prioritise actions and track improvement
Seed, root, or plant material checks when there is uncertainty about disease carry-over
Why Biomcare
Many "fungi tests" return a long list of detections without clarity on what matters. Biomcare's report is designed to support decisions by combining:
Validated, robust readout for the 9 key pathogens – one test to rule them all
A broad fungal profile for situational context
Interpretation guidance that focuses on practical risk signals-not just detection
Ready to screen fungal risk before planning next season?
Send your sample type (soil/root/plant/seed) and the crop decision you're considering. We'll recommend a simple sampling plan and deliver a report you can use for rotation and risk planning.
Quick Contact
Email us at
info at biomcare dot comCall us at
+45 31 57 20 81We typically respond within 24 hours on business days.
Scientific Responsibility
Scientific responsibility for this service lies with Louise Bruun Thingholm, PhD, Chief Scientific Officer at Biomcare. Louise provides scientific oversight and quality assurance for Biomcare's sequencing and analysis deliverables.
PhD in Bioinformatics | Clinical Microbiome Research | Founder of Biomcare
