Mycology 105: Troubleshooting, Optimization & Scaling

You've learned the fundamentals across Mycology 101-104. Now it's time to develop the diagnostic skills and optimization mindset that separate hobbyists from serious cultivators. This guide provides frameworks for solving problems and improving results.

The Diagnostic Framework

When something goes wrong, resist the urge to guess randomly. Instead, work through a systematic diagnostic process.

Define the Problem

What exactly is wrong? "Contamination" is too vague. "Green mold appearing on grain spawn 7 days after inoculation" is specific and actionable.

Gather Data

Pull up your records. What strain? What spawn lot? What sterilization batch? What incubation conditions? The answer often hides in the details.

Identify Patterns

Is this an isolated incident or a recurring issue? Are there commonalities between failed batches?

Hypothesize and Test

Form a hypothesis about the root cause. Design a test to verify. Change one variable at a time.

Why Records Matter

Without records, troubleshooting becomes guesswork. When you can see that all contaminated jars came from the same grain batch or the same transfer session, the problem becomes obvious.

Common Problems and Solutions

Contamination Patterns

Pattern	Likely Cause	Solution
Random jars in a batch	Poor sterile technique during inoculation	Improve SAB/flow hood protocol
All jars from one batch	Under-sterilization or wet grain	Extend PC time, improve grain prep
Contamination after shaking	Loose filter discs or cracked lids	Inspect containers before use
Contamination during fruiting	Environmental spores	Improve fruiting room hygiene
Recurring same contaminant	Persistent source	Deep clean and identify source

Stalled Colonization

If mycelium stops growing or grows unusually slowly:

Temperature too low: Verify incubation temps (most species need 70-78°F)
Substrate too dry: Grain wasn't properly hydrated before sterilization
Genetic issue: Culture may be senescent (too many transfers)
Wrong substrate: Some species won't colonize certain substrates

Fruiting Problems

Symptom	Cause	Fix
No pins forming	Too much CO2	Increase FAE
Pins aborting	Humidity too low	Increase misting, check humidifier
Long stems, tiny caps	Too much CO2	Increase FAE
Overlay (thick mat, no pins)	Too rich substrate or CO2	Fork-tek, increase FAE
Bacterial blotch	Too much moisture on surface	Reduce misting, improve airflow

Yield Optimization

Once you've eliminated obvious problems, focus on optimization. Small improvements compound across hundreds of blocks.

Tracking Key Metrics

At minimum, track these for every batch:

Biological efficiency (BE): Fresh weight of mushrooms / dry weight of substrate × 100
Colonization time: Days from inoculation to full colonization
Contamination rate: Percentage of units lost to contamination
Flushes per block: Number of productive harvests

Benchmarks by Species

Species	Good BE	Excellent BE
Oyster	100-150%	150-200%
Lion's Mane	60-80%	80-100%
Shiitake	75-100%	100-125%

If you're significantly below these benchmarks, there's room for improvement in genetics, substrate, or conditions.

Optimization Levers

Genetics: The single biggest lever. A high-yielding strain can outperform a mediocre one by 50-100%. Test multiple isolates and keep records.

Substrate formulation: Experiment with supplementation rates. More nitrogen (soy hulls, bran) increases yield but also contamination risk.

Environmental tuning: Small improvements in humidity, temperature, or FAE consistency can meaningfully impact yield.

Spawn rate: Higher spawn rates mean faster colonization and lower contamination risk, but higher cost. Find your optimal balance.

Change One Variable

When experimenting, change only one variable at a time. Otherwise, you won't know which change caused the improvement.

Strain Selection and Testing

Not all genetics are equal. Develop a systematic approach to evaluating strains.

Evaluation Criteria

Criterion	Why It Matters
Yield	Direct revenue impact
Colonization speed	Faster turnover, less contamination window
Morphology	Market preference for shape and size
Shelf life	Post-harvest quality retention
Contamination resistance	Reduces losses

Testing Protocol

Start with 5+ isolates of the same species
Run each through identical conditions
Track all metrics for at least 3 fruiting cycles
Select top performers for production
Archive winning genetics

Your best strain today may not be your best in a year. Continuous testing and selection improve your operation over time.

Scaling Considerations

Moving from hobby to small commercial production involves more than just buying bigger equipment.

Space Requirements

Scale	Space Needed	Notes
Hobby (10 blocks/week)	Spare room or closet	Minimal infrastructure
Side business (50 blocks/week)	Dedicated room or garage	Basic climate control
Small commercial (200+ blocks/week)	Purpose-built facility	Professional systems

Process Documentation

At scale, consistency requires documented procedures:

Standard Operating Procedures (SOPs): Step-by-step instructions for every task
Batch records: Complete documentation of each production run
Quality checklists: Verification points throughout the workflow
Training materials: For bringing on help

Regulatory Considerations

Commercial food production has regulatory requirements. Research your local food safety regulations before selling mushrooms.

The Data Advantage

Commercial operations that track everything outcompete those flying blind:

Identify which strains perform best in your conditions
Spot contamination sources before they become patterns
Optimize substrate formulations based on actual results
Make informed decisions about genetics and process changes

Log each production batch, record your harvests, and review the data regularly. The cultivators who measure, improve.

Building Your Continuous Improvement Cycle

Excellence in cultivation isn't a destination—it's a process.

Measure

Track key metrics for every batch: colonization time, contamination rate, yield.

Analyze

Review data weekly or monthly. Look for trends, outliers, and patterns.

Hypothesize

Form theories about what's working and what isn't based on your data.

Experiment

Test one variable at a time. Run controlled comparisons.

Implement

When you find improvements, update your SOPs and make them standard.

Repeat

This cycle never ends. There's always room to improve.

The Complete Curriculum

You've now completed the Mycology 101-105 series. From basic biology through advanced troubleshooting, you have the knowledge foundation for successful cultivation. Now it's time to apply it.

Quick Reference: Troubleshooting Checklist

When problems occur:

Document the specific symptoms
Review batch records for the affected items
Check for patterns across multiple batches
Verify environmental conditions are within range
Inspect equipment for issues (filters, seals, etc.)
Review recent process changes
Form hypothesis and design test
Implement fix and monitor results