Citation: Alotaibi, F.; Lee, S.-J.; Lahrach, Z.; St-Arnaud, M.; Hijri, M. Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum- Hydrocarbon-Contaminated Soil. Microorganisms 2023, 11, 2972. https://doi.org/10.3390/ microorganisms11122972 Academic Editor: Nikolay Bojkov Vassilev Received: 24 October 2023 Revised: 30 November 2023 Accepted: 10 December 2023 Published: 12 December 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). microorganisms Brief Report Draft Genome of Nocardia canadensis sp. nov. Isolated from Petroleum-Hydrocarbon-Contaminated Soil Fahad Alotaibi 1,2, * , Soon-Jae Lee 1,† , Zakaria Lahrach 1,3 , Marc St-Arnaud 1 and Mohamed Hijri 1,3, * 1 Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 East Sherbrooke St., Montréal, QC H1X 2B2, Canada; soon-jae.lee@unil.ch (S.-J.L.); zakaria.lahrach.1@umontreal.ca (Z.L.); marc.st-arnaud@umontreal.ca (M.S.-A.) 2 Department of Soil Science, King Saud University, Riyadh 11564, Saudi Arabia 3 African Genome Center, University Mohammed VI Polytechnic (UM6P), Ben Guerir 43150, Morocco * Correspondence: fanalotaibi@ksu.edu.sa (F.A.); mohamed.hijri@umontreal.ca (M.H.) † Present address: Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland. Abstract: The bacterial strain WB46 was isolated from the rhizosphere of willow plants (Salix purpurea L.) growing in soil contaminated with petroleum hydrocarbons. The strain was subjected to whole- genome shotgun sequencing using Illumina HiSeq. Its draft genome is 7.15 Mb, with a 69.55% GC content, containing 6387 protein-coding genes and 51 tRNA and 15 rRNA sequences. The quality and reliability of the genome were assessed using CheckM, attaining an estimated genome completeness of 98.75% and an estimated contamination of 1.68%. These results indicate a high-quality genome (>95%) and low contamination (<5%). Many of these genes are responsible for petroleum hydrocarbon degradation, such as alkane 1-monooxygenase (alkB) and naphthalene dioxygenase (ndo). 16S rRNA gene analysis, including in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI), showed that strain WB46 belongs to the genus Nocardia, and the most closely related species is Nocardia asteroides. The strain WB46 showed a distance of 63.4% and sequence identity of 88.63%, respectively. These values fall below the threshold levels of 70% and 95%, respectively, suggesting that the strain WB46 is a new species. We propose the name of Nocardia canadensis sp. nov. for this new species. Interestingly, the sequence divergence of the 16S rRNA gene showed that the divergence only occurred in the V2 region. Therefore, the conventional V3–V4, V5–V7, or V8–V9 targeting metabarcoding, among others, would not be able to assess the diversity related to this new species. Keywords: alkane 1-monooxygenase (alkB); alkanes; genome sequencing; Nocardia canadensis; plant- growth-promoting rhizobacteria 1. Introduction Intensive industrial activities, such as extracting oil and gas, employing inorganic fertilizer-based agriculture, mining for minerals, and disposing of industrial waste, are as- sociated with risks of environmental contamination, which present a global challenge [1,2]. Of particular concern are petroleum hydrocarbons (PHCs), which can result in high-risk oil spills and environmental contamination in both aquatic and terrestrial ecosystems [3,4]. PHCs, such as crude oil, are heterogeneous organic mixtures composed of carbon and hydrogen atoms, split into two major fractions: aliphatic hydrocarbons (alkenes, alkynes, or alkanes) and aromatic hydrocarbons (including monoaromatic and polycyclic aromatic hydrocarbons (PAHs)) [5]. Most commonly, the sources of PHC contamination are anthro- pogenic, derived from accidental release (e.g., diesel, fuel, solvents) and industrial activities (e.g., electricity production, petrochemical) [6]. Such environmental contamination with PHC products has caused significant detriment to various ecosystems, including soils, with serious economic consequences [7]. Microorganisms 2023, 11, 2972. https://doi.org/10.3390/microorganisms11122972 https://www.mdpi.com/journal/microorganisms