ABSTRACT
We report the draft genome sequences of Bacillus glennii V44-8, Bacillus saganii V47-23a, and Bacillus sp. strain V59.32b, isolated from the Viking spacecraft assembly cleanroom, and Bacillus sp. strain MER_TA_151 and Paenibacillus sp. strain MER_111, isolated from the Mars Exploration Rover (MER) assembly cleanroom.
ANNOUNCEMENT
Three strains used in this study, Bacillus glennii V44-8, Bacillus saganii V47-23a, and Bacillus sp. strain V59.32b, were isolated from the vehicle assembly building (VAB) at Cape Canaveral, Florida, where the Viking spacecraft were assembled (1). Teflon ribbons were left out for 7 days to collect airborne microorganisms and then exposed to a total of 6 different heat treatments at 3 different time cycles (2). The other 2 isolates, Bacillus sp. strain MER_TA_151 and Paenibacillus sp. strain MER_111, were isolated from the Mars Exploration Rover (MER) cleanroom.
All 5 strains were cultured in tryptic soy agar (TSA) medium at 32°C for 48 h, and the DNA was extracted using an automated DNA extraction instrument (Maxwell 16, Promega, USA). An Illumina TruSeq DNA PCR-free library preparation kit (350-bp insert size) was used following the manufacturer’s instructions, and paired-end Illumina sequencing was performed on the HiSeq 2500 platform at Psomagen (Rockville, MD, USA). The raw reads were processed with CLC Genomics Workbench v10.1.1, using the default parameters for performing filtering and trimming of adapters and ambiguous nucleotides. The assembly k-mer size was optimized based on the N50 scores. The quality of the assembled genomes was assessed using QUAST v4.0 (3). The genome statistics were analyzed using Bioinformatic Tools v1.4.71 (4), and the estimated completeness and contamination were evaluated using CheckM v1.1.2 (5). The genomes were subsequently annotated using the NCBI PGAP pipeline v4.6 (V44-8, V47-23a, and V59.32b) and v4.9 (MER_TA_151 and MER_111) (6). See Table 1 for information on the assemblies and for the annotation summaries of the five strains.
Sequencing and assembly metrics and NCBI PGAP annotation data for bacterial strains
The taxonomic assignments of B. glennii and B. saganii were determined based on a polyphasic study, including the biochemical, phylogenetic, and phenotypic characteristics (1). GToTree v1.4.11 (7) was used to create a phylogenomic tree with NCBI-designated representative genomes (as accessed on 14 February 2020) of Bacillus and Paenibacillus based on the concatenated alignments of 119 single-copy core genes specific to the Firmicutes phylum (default settings used other than “-H Firmicutes”) (8–14). The genus-level taxonomies of the Paenibacillus isolate, Bacillus sp. strain V59.32b, and Bacillus sp. strain MER_TA_151 were determined by their positions in the phylogenetic tree (as shown in https://doi.org/10.6084/m9.figshare.12245441). We were unable to assign species-level taxonomy to these isolates due to the known discrepancies between phylogeny and taxonomy in these genera.
Data availability.The whole-genome shotgun sequencing projects were deposited in GenBank and the raw sequencing reads in the NCBI Sequence Read Archive under the accession numbers QVTD00000000.1 and SRR11096019 (Bacillus glennii V44-8), QVTE00000000.1 and SRR11096037 (Bacillus saganii V47-23a), QVTC00000000 and SRR11097317 (Bacillus sp. strain V59.32b), VYKL00000000 and SRR11096322 (Bacillus sp. strain MER_TA_151), and VYKK00000000 and SRR11097201 (Paenibacillus sp. strain MER_111), respectively.
ACKNOWLEDGMENTS
The research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. We acknowledge Jonathan Eisen and Alvin Smith for preliminary discussions about the workshop.
We received financial support from JPL’s Center for Academic Partnership (CAP) funding. Computational resources for the course were made available by the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by NSF grant number ACI-1548526, via JetStream through allocation TG-MCB200008 (15).
FOOTNOTES
- Received 13 April 2020.
- Accepted 7 June 2020.
- Published 25 June 2020.
- Copyright © 2020 Becket et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
