A method for sampling the living wood microbiome

Efforts to characterize microbial life across diverse environments have progressed tremendously, yet the microbiome of Earth’s largest biomass reservoir—the wood of living trees has been largely unexplored. Current understanding of the tree microbiome is largely confined to roots and leaves, with little attention given to the endophytic microbiome of wood. Emergent studies have indicated this zone as a niche for unique taxa, of consequence for ecosystem health and global biogeochemical cycles. The lack of investigation derives partly from the physical recalcitrance of wood, which presents challenges during sampling, homogenization, and the extraction of nucleic acids. In response to these issues, we present an optimized method for processing wood for use in microbial analyses, from sampling through downstream PCR-based analyses. Using methane-cycling taxa as model endophytes, we assess losses in recovery during our method, and determine a limit-of-detection of approximately 500 cells pe..., , , # Data from: A Method for Sampling the Living Wood Microbiome

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Included herein is raw ddPCR (BioRad QX200 droplet reader; mix of EvaGreen and probe chemistries) data used in methods testing, broken down into the subsections from the manuscript and gene target. Some processed metadata (e.g., sample mass) is also included. Additionally, the raw sequencing files (paired end sequencing, Illumina MiSeq) for the 3 sequenced red maple heartwood samples is included (both forward and reverse reads).

Empty entries later categorized as NA or NULL during R processing.

***Raw ddPCR Data from QX200***

**zymo_1_24_test_core_pmoA_20220616_205334_819.csv,**

**Tree_Methods_pmoA_Eva_20230226_210141_169.csv,**

**Tree_Methods_mmoX_EvaGreen_20230301_194341_834.csv,**

**Tree_Methods_mcrA_EvaGreen_20230228_173602_437.csv,**

**Methods_Tree_Serial_Dil_mcrA_P_20230302_214357_917.csv,**

**Methods_Plate_mcrA_Probe_20230223_182334_914.csv,**

**Methods_plate_mcrA_FAM_redos_20230225_233035_079.csv,**...