Supplementary code and data for: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee

Host-microbe interactions underlie the development and fitness of many macroorganisms, including bees. Whereas many social bees benefit from vertically transmitted gut bacteria, current data suggests that solitary bees, which comprise the vast majority of species diversity within bees, lack a specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of the ground-nesting solitary bee Anthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacterial genera (Streptomyces, Nocardiodes) and the fungus Moniliella spathulata. Dormant (diapausing) larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for diapausing bees. First, using isolated bacteria and fungi, we found that Streptomyces..., This dataset includes data and code for the following: amplicon sequencing (1A), qPCR (1B), plate inhibition (2), and sugar/sugar alcohol analysis (3). Software and major package versions: R (4.1.1), DADA2 (1.22.0), phyloseq (1.38.0), vegan (2.6.4), microbiome (1.23.1), and ggplot2 (3.4.2). For furhter method details see manuscript.

Amplicon data and qPCR are from stages throughout the lifecycle of a solitary bee, as well as environmental samples. All samples were added whole to DNA extraction, following preprocessing. Extraction for all samples was done per manufacturer’s instructions with the DNeasy PowerSoil Pro kit. Four blanks were included in DNA extractions. Extracted DNA was stored in the included extraction buffer at -80oC for amplicon sequencing and qPCR.

 Amplicon sequencing of extracted DNA was done to assess bacterial and fungal community composition using the 16S rRNA (V5/6) gene and ITS gene at the Integrated Microbiome Resource (IMR) at Dalhousie University in Halifax,..., , # Supplementary Code and Data for: *Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee*

[https://doi.org/10.5061/dryad.gtht76ht1](https://doi.org/10.5061/dryad.gtht76ht1)

This dataset contains data and code in three files: **\"Supplemental code and data.zip\"** contains all of the files and folders listed below. **\"16Srawfiles.zip\"** and **\"ITSrawfiles.zip\"** contain the raw bacterial and fungal data for use in the \"Amplicon\" subfolder once you open the \"Supplemental code and data.zip\" (as listed below).

## Raw Illumina Amplicon Data

**\"16Srawfiles.zip\"** and **\"ITSrawfiles.zip\"** unzip to folders which each contain the raw forward and reverse \".fastq.gz\" files from the Illumina sequencing of each sample for bacteria (16S) and fungi (ITS), respectively. The file names correspond to sample number (ex. \"Sample15\" or \"S140\") and forward (\"R1\") or reverse (\"R2\") reads. This raw data is used in the Amplicon R code below.

This ...