ABSTRACT
Aminobacter carboxidus is a soil Gram-negative alphaproteobacterium belonging to the physiological group of carboxydobacteria which aerobically oxidize CO to CO2. Here, we report the draft genome sequence of the A. carboxidus DSM 1086 type strain and the identification of both form I and form II CO dehydrogenase systems in this strain.
ANNOUNCEMENT
Aminobacter carboxidus DSM 1086T (basonym Carbophilus carboxidus), formerly known as Achromobacter carboxydus (1) or Alcaligenes carboxydus (2), is the type strain and the unique known member of the species (3, 4). It was isolated from soil near a stream in Moscow, Russia (1), and was assigned to the physiological group of carboxydobacteria due to its ability to grow aerobically on carbon monoxide (CO) as the sole carbon and energy source (1, 5). Carbon monoxide dehydrogenase (CODH) activity, which is responsible for the oxidation of CO to carbon dioxide (CO2), was formerly detected in A. carboxidus DSM 1086T (6). Two CODH forms are known; form I specifically oxidizes CO, whereas form II is a putative CODH with a lower affinity for CO and still uncertain function (7, 8). Carbon dioxide produced by CO oxidation can be assimilated through the Calvin-Benson-Bassham cycle, although A. carboxidus is a facultative chemolithotroph able to utilize a wide variety of organic substrates for heterotrophic growth (5). Here, the genome sequence of A. carboxidus DSM 1086T is reported with the aim of providing helpful insights into the genetic basis of CO oxidation in this monotypic strain.
A. carboxidus DSM 1086T was obtained from DSMZ and aerobically grown at 30°C in Trypticase soy broth. DNA extraction was performed using a QIAamp DNA minikit (Qiagen). A genomic library of A. carboxidus was obtained with the TruSeq DNA PCR-free sample preparation kit (Illumina, Inc., San Diego, CA, USA). Genome sequencing was performed with a NextSeq 500 sequencing system (Illumina, UK) according to the manufacturer’s protocol, and library samples were loaded into a midoutput kit v2.5 (300 cycles) (Illumina, UK), producing 1,416,277 pairs of reads. Raw sequence reads were filtered and trimmed using the command-line fastq-mcf software (https://expressionanalysis.github.io/ea-utils/). Fastq files of Illumina paired-end reads (150 bp) were used as input in the MEGAnnotator pipeline for microbial genome assembly and annotation (9). This pipeline employed the SPAdes program v3.14.0 for de novo assembly of the genome sequence with the option “--careful” and a list of k-mer sizes of 21, 33, 55, 77, 99, and 127 (10). The genome quality was evaluated with the program CheckM (11), estimating a genome completeness of 99.3%. The contigs were then submitted to the National Center for Biotechnology Information (NCBI) for the prediction of protein-encoding open reading frames (ORFs) and tRNA and rRNA genes using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (12). All tools were run with default parameters unless otherwise specified.
The draft genome of A. carboxidus is 6,291,275 bp long. It was assembled into 31 contigs with an N 50 value of 458,931 bp, an average coverage of 65×, and a mean GC content of 62.96%. Genome annotation identified 6,023 ORFs, 49 tRNA genes, and 3 rRNA genes. Two gene clusters predicted to encode both forms of heterotrimeric CODH were identified (Fig. 1). Form I showed the specific AYXCSFR signature in CoxL and six accessory genes (coxDEFGHI) flanking the coxMSL structural genes, whereas form II showed the typical coxSLM structural gene arrangement and the specific AYRGAGR signature in CoxL.
Forms I and II of the cox gene clusters in A. carboxidus DSM 1086T. (A) The putative cox genes encoding form I and form II of the heterotrimeric (αβχ)2 CODH enzyme complex (CoxL, CoxM, and CoxS subunits) of A. carboxidus DSM 1086T with their GenBank annotation, gene name, and closest ortholog. KEGG Orthology numbers were assigned with the KEGG Automatic Annotation Server (KAAS) (13). (B) Physical map of the A. carboxidus DSM 1086T genomic regions encompassing the form I (contig 11) and form II (contig 7) cox gene clusters. Form I is characterized by three structural genes, in the order coxMSL (gray), followed by six accessory genes (white), and by the presence of the AYXCSFR motif in the predicted CoxL active site. A different order of the three structural genes, coxSLM (gray), is characteristic of form II, and the CoxL active site contains the typical AYRGAGR motif.
Data availability.This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession number JACZEP000000000. The version described in this paper is JACZEP000000000.1. The raw sequencing reads are available at the Sequence Read Archive under accession number SRR12759717 and are associated with BioProject number PRJNA666410.
ACKNOWLEDGMENTS
This work was supported by the Excellence Departments grant (art. 1, commi 314-337 Legge 232/2016) to the Department of Science, Roma Tre University, and grant PRIN 2017 (Prot. 20177J5Y3P) to P.V., both from the Italian Ministry of Education, University and Research (MIUR).
FOOTNOTES
- Received 8 October 2020.
- Accepted 22 October 2020.
- Published 5 November 2020.
- Copyright © 2020 Turrini et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
