DOI: 10.5061/dryad.x3ffbg7zc
title: Data from: Bacterial and fungal growth on fungal necromass and its diverse components: shared profiles and divergent constraints revealed by high-throughput phenotyping

description: While fungal necromass is increasingly recognized as a major source of
 persistent carbon (C) in soils, the relative functional roles of bacteria
 and fungi in decomposing necromass are not fully resolved, and the
 processes that select for necromass decomposer communities from the
 broader soil microbial community are an emerging area of interest. In this
 study, we characterized the growth of 52 bacterial and 83 fungal strains
 isolated from necromass and soil on 22 C substrates, including different
 necromass phenotypes, fungal cell wall polymers, dimers, and monomers. We
 found that isolation habitat of the strains used in this experiment
 (necromass vs. soil) had no effect on the substrates they were able to
 use. Isolates from both microbial domains were able to grow on different
 labile carbon substrates, polymers, and necromass phenotypes. However,
 fungal growth was limited by necromass melanin content while bacterial
 growth was more limited by the abundance of cell wall polysaccharides.
 Additionally, overall differences in substrate use between bacteria and
 fungi were most pronounced on polymer substrates. Collectively, our
 results suggest that there is substantial functional overlap in necromass
 substrate use across microbial domains, but some notable differences in
 bacterial and fungal utilization of cell wall polymers, which can function
 as a direct energy source or a means of accessing other compounds within
 necromass. Future studies assessing bacteria and fungi decomposing
 necromass together rather than in isolation will help to uncover potential
 physical and chemical interactions within and between these two domains
 during the decay of this important source of persistent soil C.
description: # Bacterial and fungal growth on fungal necromass and its diverse
 components: shared profiles and divergent constraints revealed by
 high-throughput phenotyping Dataset DOI:
 [10.5061/dryad.x3ffbg7zc](10.5061/dryad.x3ffbg7zc) ## Description of the
 data and file structure This dataset documents the substrate utilization
 of 52 bacterial and 83 fungal strains isolated from a pine forest plot at
 the Cedar Creek Ecosystem Science Reserve. The optical density of each
 strain on a given substrate was used to quantify total growth across 22
 carbon substrates. Additionally this dataset includes files generated from
 16S and ITS high throughput sequencing at the same forest plot from which
 the strains were isolated, including bacterial and fungal OTUs files and
 taxonomic assignments.  ### Files `bact_norm.csv`: This file documents
 bacterial growth data, including strain name and taxonomic information,
 substrate names and groupings, isolation habitat of strains, and growth
 (as optical density) on each substrate. `fungal_norm.csv`: This file
 documents fungal growth data, including strain name and taxonomic
 information, substrate names and groupings, isolation habitat of strains,
 and growth (as optical density) on each substrate.
 `microbial_norm_nmds.csv`: This file documents microbial growth data of
 each strain on each substrate normalized by growth across all substrates
 formatted for NMDS analysis by domain `bacteria_taxonomy.csv`: This file
 documents taxonomy of OTUs generated by bacterial high-throughput
 sequencing of soil communities at Cedar Creek Ecosystem Science Reserve
 from necromass bags and surrounding soil. `fungi_taxonomy.csv`: This file
 documents taxonomy of OTUs generated by fungal high-throughput sequencing
 of soil communities at Cedar Creek Ecosystem Science Reserve from
 necromass bags and surrounding soil. `bacteria_rarefied_otu_mapping.csv`:
 This file contains rarefied bacterial OTU tables
 `fungi_rarefied_otu_mapping.csv`: This file contains rarefied fungal OTU
 tables `FTIR_peaks.csv`: This file contains FTIR peak absorbance data for
 each of the four necromass phenotypes tested ### Variables and
 abbreviations: * Strain: Strain identifiers  * Substrate: Carbon
 substrates analyzed. Note that NAG = N-acetyl-glucosamine, L-DOPA =
 l-3,4-dihydroxyphenylalanine, HighMel refers to high melanin necromass,
 LowMel refers to low melanin necromass, WC denotes whole cell (unwashed)
 necromass, and CW denotes the cell wall (washed) necromass type.  *
 SubstrateGroup: Categorization of a substrate as one of three groups:
 Soluble (specifically monomers and dimers), Polymer, or Necrotype
 (necromass phenotypes).  * Habitat: Habitat from which strain was isolated
 (one of three options: high melanin necromass, low melanin necromass, or
 soil).  * Phylum: Phylum of strain or OTU * Class: Class of strain or OTU
 * Order: Order of strain or OTU * Family: Family of strain or OTU * Genus:
 Genus of strain or OTU * Species: Species of strain or OTU * BinGrowth:
 Binary indicator column, with 1 indicating growth on a substrate and 0 no
 growth. A threshold of ∆ OD &gt; 0.1 was used to determine growth.  *
 NormalizedOD: Optical density at a 600nm wavelength, normalized by
 controls and blanks.  * Avg_growth_all_subs: Average growth of a strain
 across all substrates in all replicates * Avg*_*growth_norm: Average
 growth of a strain on a given substrate, normalized by average growth
 across all substrates.  * Log_avg_norm: Log(x+1) transformation of
 Avg_growth_norm * Domain: Domain of strain (either bacteria or fungi) *
 Necrotype: Necromass type (one of four phenotypes: High melanin WC, Low
 melanin WC, High melanin CW, Low melanin CW)  * Sample_ID: Name of sample
 with replicate number * Peak X: FTIR peak wave number (cm^-1), as called
 by Origin Lab * Peak Y: Height (absorbance) of the FTIR peak, as called by
 Origin Lab * peak*_*maillard*_*paper: Peak wave numbers annotated
 according to Maillard, Pflender, et al. 2023 * Functional group: Bond
 types of peaks * Melanization: Melanin content in necromass (high vs. low
 melanin) * wall_status: Necromass cell wall type (cell wall vs. whole
 cell) ## Code/software All data were analyzed and visualized in R 4.3.0 (R
 Core Team 2023). We used the lme4 and lmerTest packages to run linear
 mixed models on the growth data and the emmeans package for posthoc tests.
 We used the vegan package for all analysis of microbial sequencing data. 
 ## Access information Other publicly accessible locations of the data: *
 n/a Data was derived from the following sources: * n/a