Formica exsecta comparison of the bacterial and fungal microbiomes of nest material and the ants

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.

Methods
We sampled F. exsecta 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 et al., 2018, PeerJ 6: e5289.). The reads were filtered and OTUs clustered (at 97% identity) using UPARSE v.8.1 (Edgar, 2013, Bioinformatics 34: 2371–2375; Edgar and Flyvbjerg, 2015, Bioinformatics 31: 3476–3482). The SILVAv132 (Quast et al., 2013, Nucleic Acids Res 41: 590–6), and the UNITE v7.2 (Kõljalg et al., 2013, Mol Ecol 22: 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 et al., 2007, Appl Environ Microbiol 73: 5261–7), and RDP ITS Warcup training set v4 (fungi) (Deshpande et al., 2016, Mycologia 108: 1–5).

本研究聚焦红褐林蚁（Formica exsecta）的微生物组（microbiome），并将其与蚁巢基质中的微生物组进行对比。我们发现，蚂蚁与其蚁巢基质之间的细菌群落与真菌群落均存在根本性差异，但不同蚁群间的细菌、真菌群落并无显著差异。蚂蚁体内细菌的物种多样性、物种丰富度及均匀度均显著低于蚁巢基质中的细菌；而就真菌而言，仅物种丰富度在蚂蚁体内低于蚁巢基质。不同蚁群的蚂蚁之间未发现此类差异。

方法
我们于2011年6月至2015年8月间的不同年份，从芬兰西南部特瓦尔明内群岛的6个蚁群中采集红褐林蚁工蚁，每个蚁群采样2-4次，总计获得18份样本，每份样本包含约15只工蚁。在同一时间段内，我们还从其中5个蚁群采集了蚁巢基质样本，其中1个蚁群在不同年份采集了2份样本。
提取得到的DNA送至Illumina MiSeq平台进行测序。文库构建、测序及生物信息学分析流程均参照（Lindström等，2018，PeerJ 6: e5289.）完成。使用UPARSE v.8.1（Edgar，2013，Bioinformatics 34: 2371–2375；Edgar与Flyvbjerg，2015，Bioinformatics 31: 3476–3482）对测序读长进行过滤，并以97%的序列相似度阈值聚类为操作分类单元（OTU，Operational Taxonomic Unit）。分别采用SILVAv132数据库（Quast等，2013，Nucleic Acids Res 41: 590–6）与UNITE v7.2数据库（Kõljalg等，2013，Mol Ecol 22: 5271–5277）作为细菌与真菌序列比对的参考数据库。分类学注释环节，我们分别使用RDP 16S训练集16 v2.12（用于细菌序列）（Wang等，2007，Appl Environ Microbiol 73: 5261–7）以及RDP ITS Warcup训练集v4（用于真菌序列）（Deshpande等，2016，Mycologia 108: 1–5）完成分类注释。