Drawing of Suillus ectomycorrhizha, spores; soil nematode, fungus, bacteria, protists; plant grass rhizosphere network

High-throughput amplicon sequencing

Illumina amplicon sequencing protocol v1.1
Nguyen Lab Illumina dual-index ITS, 16S, and 18S primers
PCR dilutions & library normalization for amplicon library preps
Peter Kennedy's useful discussion on fungal amplicon sequencing
Nhu Nguyen's discussion on the use of exact sequence variants (ESV) for fungal ITS

Molecular protocols

Short CTAB DNA extraction - relatively quick and clean DNA products from fresh tissues, cultures, or dried specimens
DNA extraction from whole root systems - good for root microbiome studies
DNA extraction protocol for tropical & volcanic soils - useful for extracting from "difficult" soils
DNA extraction protocol for high molecular weight (>25kb) molecules from fungal tissue
Quick DNA extraction for PCR from single specimens - good for specimens or microbial cultures
SPRI magnetic bead DNA cleanup & size selection

Buffer & media recipes

Loading dyes for electrophoresis
2% CTAB recipe - for use in standard nucleic acid extractions
Sodium borate (SB) Buffer - for electrophoresis
Hoagland's solution - for plant culture

Specimen-based sequencing for systematics

Mushroom data template form - keep track of specimens, formatted for MycoPortal & GenBank
GenBank source modifier table - keep track of sequence data, import into sequin for submission to GenBank.

Tissue staining

PDAB solution for mushroom identification
Rose Bengal stain for soil microbes
Arbuscular mycorrhizal fungi (AMF) staining protocol

Miscellaneous protocols & manuals

Spore extractions directly from bolete pores
Manual for yeast work from Meredith Blackwell's lab
Beetle dissection for gut microbial studies