DOI: 10.5061/dryad.8931zcs07
title: Data from: The relationship between microbial community succession, decay, and anatomical character loss in non-biomineralized animals

description: A  fundamental assumption of hypothesis-driven decay experiments
 is that, during decay, the loss of anatomy follows a sequence broadly
 controlled by the intrinsic compositional properties of tissues. Recent
 work investigating the succession of postmortem endogenous microbial
 communities (thanatomicrobiome) challenges this assumption. These studies
 suggest the internal thanatomicrobiome exhibits a predictable succession
 in response to physical and chemical environmental changes that occur
 within a carcass. Therefore, it is possible that reproducible sequences of
 character loss during decay are controlled by thanatomicrobiome succession
 dynamics. If so, exceptionally preserved fossil anatomy would reflect a
 succession of ancient contemporaneous microbial communities, about which
 we know nothing, rendering decay experiments uninformative. Here, we
 investigate two questions: (1) what is the role of exogenous and
 endogenous bacteria during formation of the thanatomicrobiome and (2) do
 thanatomicrobiome successions control the sequence of anatomical character
 loss within a decaying carcass? Our analysis shows that the internal
 thanatomicrobiome is dominated by endogenous bacteria and that, even in
 the presence of inoculum, exogenous bacteria do not invade the carcass and
 replace native bacteria (while the carcass is intact). This confirms that
 the use of environmental inoculum in decay experiments introduces an
 inadvisable confounding variable. Secondly, we find no correlation between
 thanatomicrobiome successions and the sequence of anatomical character
 loss, supporting the hypothesis that fossil non-biomineralised characters
 correlate with their propensity to decay in extant relatives. These
 findings indicate that the inability to model ancient bacteria does not
 invalidate decay experiments. We also present a synthesis of the role of
 bacteria in non-biomineralised fossilisation.
description: # Data from: The relationship between microbial community succession,
 decay, and anatomical character loss in non-biomineralized animals
 [https://doi.org/10.5061/dryad.8931zcs07](https://doi.org/10.5061/dryad.8931zcs07) 7 Supplementary data files pertaining to: DNA extraction info and sample info (**1_DNA_extraction_info.xlsx**), Sample Naming conventions, Bacterial Diversity, Sample contamination, and DNA quantity and quality data (**2_OTUreads_QPCRvalues_Alpha_BetaDiversity.xlsx**), Amphioxus decay data (**3_Decay_experiment_data.xlsx**), PCoA analyses (**4_PCoA_data.xlsx**), Operational Taxonomic Unit raw data (**5_OTU_Raw_data.xlsx**), Operational Taxonomic Unit abundance per sample (**6_OTU_abundance_per_sample.xlsx**), Respiratory mode and major electron accepter data for Operational Taxonomic Units (**7_OTU_anerobic_vs_aerobic.xlsx**). ### Data and file structure 7 files organized as: **1_DNA_extraction_info.xlsx**: DNA Extraction information. **1.1. Extraction kit info** (yellow indicates DNA extraction success) * *sample code*: Sample identifier * *sample desc*: Sample description * *medium*: medium used (ASW = Artificial Sea Water) * *DNA extraction kit used*: DNA extraction kit used. **1.2. 16s Indexing primers** * *Index* * *Bases in Adaptor* * *Index Name* * *Adaptor Region* * *Index* * *Primer Segment* * *Full Index Primer Sequence* **1.3. Bacterial OTU list** * *OTU*: Operational Taxonomic Unit * *Domain* * *Phylum* * *Class* * *Order* * *Family* * *Genus* **2_OTUreads_QPCRvalues_Alpha_BetaDiversity.xlsx**: Sample Naming conventions, Bacterial Diversity, Sample contamination, and DNA quantity and quality data **2.1. Sample Names** * *Sample Code*: Sample identifier * *Medium*: medium used (ASW = Artificial Sea Water) * *Sample Day*: Day of sampling * *Reported Sample Name*: Sample name in publication **2.2. OTU reads and QPCR values** * *Sample Code*: Sample identifier * *Medium*: medium used (ASW = Artificial Sea Water) * *Sample Day*: Day of sampling * *Reported Sample Name*: Sample name in publication * *Total OTU Reads*: Total Operational Taxonomic Unit Reads * *QPCR Value*: Quantitative Polymerase Chain Reaction value * *LOG10 QPCR value*: Log10 Quantitative Polymerase Chain Reaction value * *Total OTUs Per Sample*: Total Operational Taxonomic Unit per sample **2.3. Alpha Diversity** * *Sample Code*: Sample identifier * *Medium*: medium used (ASW = Artificial Sea Water) * *Sample Day*: Day of sampling * *Total OTU Reads*: Total Operational Taxonomic Unit Reads * *QPCR Value*: Quantitative Polymerase Chain Reaction value * *LOG10 QPCR value*: Log10 Quantitative Polymerase Chain Reaction value * *Total OTUs Per Sample*: Total Operational Taxonomic Unit per sample * *Shannon's H*: Statistical test * *Shannon's Equitability*: Statistical test **2.4. Beta Diversity** * *Beta diversity data table (top)* * *Sediment beta diversity data table (bottom)* **2.5 QPCR Contamination** * *QPCR contamination values* **2.6 DNA quantity and quality** * *Sample Code*: Sample identifier * *Medium*: medium used (ASW = Artificial Sea Water) * *Sample Day*: Day of sampling * *DNA Quantity Qubit Values (ng/µl)*: Concentration of DNA. '-' indicate sample failure. * *DNA Quality Ratio of Absorbance A260/A230*: DNA Purity measurement. '-' indicate sample failure. * *DNA Quality Ratio of Absorbance A260/A280*: DNA Purity measurement. '-' indicate sample failure. **3_Decay_experiment_data.xlsx**: Amphioxus decay data (character presence/absence) Anatomical character decay (left column) data through time (sampling points: 2, 21, 28, 35, and 134 days). '1' = character present, 0 = character lost (decayed). Completeness = average characters remaining. **4_PCoA_data.xlsx**: data used for PCoA analyses **4.1. Bact comm structure PCoA** Table showing Bacterial community structure PCoA coordinates, percent, and eigenvalues for each sample. **4.2. Seq of character loss PCoA** Table showing sequence of Amphioxus character loss (i.e. decay) PCoA coordinates, percent, and eigenvalues for each sample. **4.3. Spearman's rank Bac_Community** Table showing Spearman's rho and p values for coordinates of decay sequence (Dec Seq) vs. Bacterial Community (Bac Com). **4.4. Spearmans PCoA Comp vs Time** Table showing Spearman's rho and p values for coordinates of decay sequence (Dec Seq) vs. Completeness and Bacterial Community (Bac Com) vs. Time. **5_OTU_Raw_data.xlsx**: Operational Taxonomic Unit raw data **5.1. Raw data** Raw output from Illumina HiSeq. Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain* * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *Taxon code*: concatenation of taxonomic ranks into one word * *value_SAMPLENAME*: raw Operational Taxonomic Unit counts * *Proportion_Genus_SAMPLENAME*: Proportion of this OTU per sample by genus * *%_Genus_SAMPLENAME*: Percentage of this OTU per sample by genus * *QPCR_SAMPLENAME*: QPCR value per sample * *Absolute_#_SAMPLENAME*: %_Genus_SAMPLENAME multiplied by QPCR_SAMPLENAME * *p*LNp_SAMPLENAME*: Natural Log value of Proportion_Genus_SAMPLENAME * *#Genera_SAMPLENAME*: binary genera presence in sample: 1 = yes. 0 = no. * *P/A_SAMPLENAME*: Presence (1) or absence (0) of genera in sample **5.2. Inoculum OTUs** * *OTU*: Operational Taxonomic Unit code * *Taxon code*: concatenation of taxonomic ranks into one word * *# of sequencing reads*:number of sequencing reads * *Proportion of overall reads* * *%*: Percentage of overall reads * *PCoA Pres/Abs*: coding for presence (1) or absence (0) for PCoA * *Common name*: common name of bacteria **5.3. PCoA abundance** Table showing Bacterial Alpha Diversity and Abundance for each sample (per row). Each row shows sample name, Alpha Diversity, Abundance, medium used (ASW = Artificial Sea Water), the day sample was terminated (day of decay) and the counts of each Operational Taxonomic Unit, represented by their OTU code. **5.4. PCoA presenceabsence** Table showing Bacterial Alpha Diversity and Abundance for each sample (per row). Each row shows sample name, Alpha Diversity, Abundance, medium used (ASW = Artificial Sea Water), the day sample was terminated (day of decay) and the presence (1) or absence (0) of each Operational Taxonomic Unit, represented by their OTU code. **5.5. Total OTUs all samples** * *sample code*: Sample identifier * *medium*: medium used (ASW = Artificial Sea Water) * *Sample day* * *Total OTU Reads*: Total Operational Taxonomic Unit reads * *QPCR Value* * *LOG10 QPCR value* * *Total OTU Per Sample*: Total number of Operational Taxonomic Units per sample * *Shannon's H* * *Shannon's Equitability* **5.6. OTU abundance Artificial sea water (ASW) vs. Inoculum (Inoc)** Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain* * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *Taxon code*: concatenation of taxonomic ranks into one word * *Sample Code*: Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **5.7. OTU abund(ance) bentonite vs time** Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain* * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *Taxon code*: concatenation of taxonomic ranks into one word * *Abundance of each bacterial genus*: samples separated by day (top) and sample identifier code (below); e.g. %_Genus_AB04 (sample AB04) **6_OTU_abundance_per_sample.xlsx**: Operational Taxonomic Unit abundance per sample **6.1. OTU abundance ASW vs. Inoc ASW** Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain* * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *Taxon code*: concatenation of taxonomic ranks into one word * *Sample Code*: Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.2. Inoculum** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.3. Day 28 Baseline** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.4. Day 28 Inoculated 1** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.5. Day 28 Inoculated 2** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.6. Day 134 Baseline** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.7. Day 134 Inoculated 1** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples.. **6.8. Day 134 Inoculated 2** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.9. Day 134 Inoculated 3** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.10. Day 1138 Inoculated** Top ten bacteria proportion are separated from rest of bacteria (represented by 'OTHER'). Column naming convention: * *OTU*: Operational Taxonomic Unit * *Domain*: concatenation of taxonomic ranks into one word * *Phylum* * *Class* * *Order* * *Family* * *Genus* * *"Family" code*: repeat of Family * *Taxon code*: concatenation of taxonomic ranks into one word * *SAMPLE NAME*: sample %. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. **6.11 Compiled data**. * *Day*: Sample day * *Type*: Sample type. Sample codes with 'Baseline' are not inoculated. 'INOC' = inoculated samples. * *Taxon Code*: Genus rank taxonomy * *higher_clade*: Family rank taxonomy * *OTU*: Operational Taxonomic Unit code * *Relative proportion* **7_OTU_anerobic_vs_aerobic.xlsx**: Respiratory mode and major electron accepter data for Operational Taxonomic Units Tabs: 7.1 Master data, 7.2 Tamar inoculum, 7.3. Day 28 Baseline, 7.4. Day 28 Inoculated 1, 7.5. Day 28 Inoculated 2, 7.6. Day 134 Baseline, 7.7. Day 134 Inoculated 1, 7.8. Day 134 Inoculated 2, 7.9. Day 134 Inoculated 3, 7.10. Day 1138 Inoculated, 7.11 Compiled data. Column naming convention: * *OTU*: Operational Taxonomic Unit * *Proportion*: proportion per sample * *Anaerobic (An)/Aerobic (Ab)*: Determination of respiratory mode for each OTU. * *Electron Acceptor*: Determination of major electron acceptor for each OTU. NA = no data ### Sharing/Access information Link to other publicly accessible location of the data: https://doi.org/10.17605/OSF.IO/9CJ8M