ABSTRACT
For their food source, Trachymyrmex septentrionalis ants raise symbiotic fungus gardens that contain bacteria whose functions are poorly understood. Here, we report the genome sequences of eight bacteria isolated from these fungus gardens to better describe the ecology of these strains and their potential to produce secondary metabolites in this niche.
ANNOUNCEMENT
Fungus-growing ants (tribe Attini) form symbioses with a cultivar fungus belonging to the genus Leucoagaricus, which they grow in underground fungus gardens as their essential food source (1). Other bacteria also inhabit these fungus gardens and provide nutrients to the cultivar fungus, at least in some cases (2–5). These bacteria have the genetic potential to produce secondary metabolites that may mediate interspecific interactions in fungus gardens, although this remains poorly understood (6).
Trachymyrmex septentrionalis is the northernmost fungus-growing ant and occurs throughout the eastern United States (7). Its colonies are relatively small (∼1,000 ants/colony) and subsist largely on caterpillar frass, oak catkins, and some fresh plant material (8). The T. septentrionalis fungus garden microbiome remains poorly characterized (9). We therefore isolated several bacteria from T. septentrionalis fungus gardens and sequenced their genomes to better understand their potential functions within this symbiotic niche.
T. septentrionalis fungus gardens were collected in Florida, New Jersey, and North Carolina following established protocols (10). Fungus garden fragments were resuspended in phosphate-buffered saline (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4), and bacteria were isolated on tryptic soy agar (Difco; adjusted to pH 6) using the spread plate technique. Genomic DNA was extracted from each isolate, and their 16S rRNA genes were PCR amplified as described previously (11). PCR amplicons were Sanger sequenced at the University of Connecticut DNA Biotechnology Center, and the resulting sequences were compared to the NCBI nonredundant database (12) to identify each strain.
Genomes from eight T. septentrionalis fungus garden bacteria were sequenced at the Department of Energy Joint Genome Institute (JGI). Pacific Biosciences (PacBio) SMRTbell libraries were constructed following the manufacturer’s protocol and sequenced using a PacBio RS instrument. The resulting reads were assembled using the HGAP pipeline version 2.3.0_p5. Genes were predicted using Prodigal (13) and GenePRIMP (14) and annotated using the UniProt (15), TIGRFAMs (16), Pfam (17), KEGG (18), COG (19), InterPro (20), and IMG nonredundant (21) databases. Noncoding RNAs were annotated using tRNAScanSE (22), INFERNAL (23), and the IMG's rRNA gene models (15). Additional gene prediction and annotation were performed using the IMG's ER platform (24).
The sequenced bacteria belong to the genera Bacillus, Burkholderia, Pantoea, and Serratia and poorly resolved taxa within the families Enterobacteriaceae and Micrococcaceae (Table 1). The genome of Serratia sp. JKS000199 was assembled into a single contig and is therefore complete. All other genomes were assembled into 2 to 6 contigs and are therefore high-quality drafts. These bacteria likely include both persistent and transient colonists of T. septentrionalis fungus gardens. The genome sequences of these strains will inform future studies of their ecology in T. septentrionalis symbiosis and how secondary metabolites might mediate interspecific interactions within this niche.
GenBank accession numbers and metadata for the strains sequenced in this study
Data availability.The whole-genome shotgun projects for strains JKS000199, JKS000233, JKS000234, JKS000250, JKS000296, JKS000303, JKS001846, and JKS001869 have been deposited in DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
This research was funded by Department of Energy Joint Genome Institute grant CSP 1652, NSF grant IOS-1656475, and the University of Connecticut. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract number DE-AC02-05CH11231. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
We thank the Florida, New Jersey, and North Carolina Departments of Environmental Protection for permission and assistance with our collections on state lands. We also thank Lee Deininger, Sarah Goldstein, and Kevin Lee for their assistance collecting ants in New Jersey and North Carolina and Cameron Currie and Heidi Horn for assistance collecting ants in Florida.
FOOTNOTES
- Received 18 June 2018.
- Accepted 25 June 2018.
- Published 19 July 2018.
- Copyright © 2018 Kopac et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
