DOI: 10.5061/dryad.ht76hdrhj
title: Formica exsecta comparison of the bacterial and fungal microbiomes of nest material and the ants

description: This study explores the microbiome of the ant Formica exsecta, and
 compares this to the microbiome found in the nest material. We found
 fundamental differences in both the bacterial and the fungal communities
 between ants and their nest material, but no
 significant differences in the bacterial and fungal communities
 among colonies. Species diversity, species richness, and evenness
 were all significantly lower for bacteria in ants than in nest material,
 whereas for fungi only species richness was lower in ants, than in nest
 material. No such differences were found among ants from diffrent
 colonies.
description: We sampled <i>F. exsecta</i> workers from six
 colonies in the Tvärminne archipelago SW Finland, each on 2-4 occasions in
 different years between June 2011 and August 2015, in total 18 samples
 consisting of ~15 ants each. Within the same time frame, we also collected
 nest material from five of these colonies, with one colony represented by
 two samples taken in different years. Extracted DNA was submitted to
 Illumina MiSeq sequencing. Preparation of libraries, sequencing and
 bioinformatics pipeline were done according to (Lindström <i>et
 al.</i>, 2018, <i>PeerJ</i> <b>6</b>:
 e5289.). The reads were filtered and OTUs clustered (at 97% identity)
 using UPARSE v.8.1 (Edgar, 2013, <i>Bioinformatics</i>
 <b>34</b>: 2371–2375; Edgar and Flyvbjerg, 2015,
 <i>Bioinformatics</i> <b>31</b>: 3476–3482). The
 SILVAv132 (Quast <i>et al.</i>, 2013, <i>Nucleic Acids
 Res</i> <b>41</b>: 590–6), and the UNITE v7.2 (Kõljalg
 <i>et al.</i>, 2013, <i>Mol Ecol</i>
 <b>22</b>: 5271–5277) databases were used as reference for the
 alignment of the bacterial and fungal sequences, respectively. For
 taxonomic classification, we used the RDP16s training set 16 v2.12 
 (bacteria) (Wang <i>et al.</i>, 2007, <i>Appl Environ
 Microbiol</i> <b>73</b>: 5261–7), and RDP ITS Warcup
 training set v4 (fungi) (Deshpande <i>et al.</i>, 2016,
 <i>Mycologia</i> <b>108</b>: 1–5). 
description: Four files, two each for bacteria and fungi, one of which
 contains data for ant samples alone, and one data from ants and their
 corresponding nest material All files provide rarefied reads
 for prokaryotes or fungi, respectively, identified in the Ant&Nest
 and Ant Data. The taxonomic (nomenclature) and systematic position of the
 bacterial samples were determined based on LPSN (List of Prokaryotic names
 with Standing in Nomenclature) https://lpsn.dsmz.de/, and those of the fungal samples were based on MycoBank (https://www.mycobank.org/ (both accessed 19.12 2021).  The taxonomical and systematic assignment should be considered tentative, as these are in many cases likely to change when new data become available, and phylogenetic relationships are resolved or updated.       Candidate bacterial phyla, which have not been validly published according to the list are indicated with apostrophes (""). Taxa indicated in boldface in the Ant&Nest data were absent in the Ant data, and vice versa. In the Ant&Nest data low counts of eukaryotes (Streptophyta, Cercozoa, Chlorophyta, Ochrophyta), and Cyanobacteria were found in addition to bacteria. In the Ant data eukaryotic plant material (Streptophyta) was found in modest counts in a few samples, and green algae (Bacillariophyta) in very low counts. These are not included in the files.