Whole-genome sequencing of Aminobacterium sp. strain MB27-C1, isolated from the wastewater treatment plant of a steel mill

TL;DR

Scientists sequenced the genome of a new Aminobacterium strain from a steel mill wastewater treatment plant in China.

Contribution

The complete genome sequence of Aminobacterium sp. strain MB27-C1 is reported for the first time.

Findings

The genome is a single contig of 2,427,830 base pairs.

The GC content of the genome is 41.58%.

Abstract

Here, we report the complete genome sequence of Aminobacterium sp. strain MB27-C1, which was isolated from sewage sludge collected at the wastewater treatment plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB27-C1 is a single contig of 2,427,830 bp with 41.58% GC content.

Figures

Neighbor-joining tree based on 16S rRNA gene sequences of strain MB27-C1 and related taxa. The phylogenetic tree was constructed using MEGA11 software (6). Bar, 0.02 substitutions per nucleotide position. Bootstrap values were expressed as percentages of 1,000 replications.

Tables

TABLE 1. Basic characteristics of Aminobacterium sp. strain MB27-C1 based on MIGS (Minimum Information for Genome Sequence) recommendation and general information on its genome

Item	Description
MIGS data
NCBI BioProject	PRJNA1006156
NCBI BioSample	SAMN37010248
GenBank accession number	CP133089
Geographic location	Sewage sludge of wastewater treatment plant of Sanming Steel Co. Ltd., Sanming, Fujian, China
Latitude and longitude	26.2649 N, 117.6245 E
Collection date	25 June 2021
Sequencing platforms	DNBSEQ-T7 and Oxford Nanopore MinION
Assembly method	Canu v. 2.2
Coverage	1,018.0×
Finishing strategy	Complete
General features of strain
Classification	Domain: BacteriaPhylum: SynergistotaClass: SynergistiaOrder: SynergistalesFamily: SynergistaceaeGenus: Aminobacterium
Gram stain	Positive
Cell shape	Rod-shaped
Relationship to oxygen	Anaerobic
Optimal growth temperature	40°C
Optimal growth pH range	7
Optimal growth NaCl concentration	1.0%
Genomic features
Size (bp)	2,427,830 bp
GC content (%)	41.58
CDSsb	2,272
Number of tRNAs	48
Number of rRNAs	3, 3, 3 (5S, 16S, 23S)
antiSMASH result	One RiPP-like gene clustera

Full text

ANNOUNCEMENT

Strain MB27-C1 was isolated from sewage sludge collected from the wastewater treatment plant of Sanming Steel Co. Ltd., located in Fujian, China, on 25 June 2021. Approximately 1 mL of sludge was directly inoculated into liquid anaerobic modified DSM924 media without acetate and formate. After incubation at room temperature (~25°C) for 2 weeks, the isolation, purification as well as 16S rRNA amplification and sequencing were conducted on the enrichment culture according to the methods described in our previous study (1). Based on the analysis using Nucleotide BLAST (2), one of the isolates, designated as strain MB27-C1, showed the highest similarities to three validly characterized strains: Aminobacterium thunnarium OTA 102^T^ (NR_178662.1, 98.47%) (3), Aminobacterium colombiense ALA-1^T^ (NR_074624.1, 95.92%) (4), and Aminobacterium mobile ILE-3^T^ (NR_024925.1, 91.25%) (5). In addition, phylogenetic analysis of 16S rRNA gene sequences performed by MEGA11 (6) for strain MB27-C1 and related taxa indicates that strain MB27-C1 belongs to the genus Aminobacterium (Fig. 1). The genome of strain MB27-C1 was sequenced for species delineation and comparative genomic analysis.

Neighbor-joining tree based on 16S rRNA gene sequences of strain MB27-C1 and related taxa. The phylogenetic tree was constructed using MEGA11 software (6). Bar, 0.02 substitutions per nucleotide position. Bootstrap values were expressed as percentages of 1,000 replications.

Strain MB27-C1 was cultured in modified DSM 924 medium at 35°C for 2 days. The genomic DNA was extracted from a cell pellet collected from a 1-L culture using the NucleoBond HMW DNA kit (Macherey-Nagel, Germany) following the manufacturer’s instructions. The genome was sequenced at the Sangon Biotech (Shanghai) Co., Ltd. using the DNBSEQ-T7 platform (MGI Tech Co., Ltd.) and the MinION sequencer (Oxford Nanopore Technology).

For the DNBSEQ-T7 platform, sheared genomic DNA fragments of approximately 300 bp were employed to construct a 150-bp paired-end DNA library. The library preparation was performed using Hieff NGS MaxUp II DNA Library Prep Kit for Illumina from Yeasen Biotechnology (Shanghai) Co., Ltd. Subsequently, the constructed library underwent sequencing using MGISEQ-2000RS High-throughput Sequencing Set (PE150 format), generating a total of 11,227,458 reads, which were then trimmed using Trimmomatic v0.36 (7). In the case of the MinION sequencer, the sheared DNA fragments underwent a series of processing steps, including end repair, 3′ adenylation (NEBNext End Repair/dA-Tailing Module), and ligation to adaptors pre-loaded with motor proteins (NEBNext Quick Ligation Module). The resulting product was then purified using Agencourt AMPure XP Beads (Beckman, A63881). Subsequently, fragments larger than 1 kb were subjected to single-molecule nanopore DNA sequencing using the Multiplex Ligation Sequencing Kit (SQK-MLK111.96-XL) on a MinION Flow Cell (R9.4.1). Basecalling was performed using Guppy version 6.5.6 with the default model, yielding a total of 115,526 reads and N50 of 6,328 bp. Trimming of the reads was carried out using Porechop v0.2.4 (8), and filtering was executed with NanoFilt v2.8.0 (9). DNBSEQ-T7 and MinION reads were hybrid de novo assembled using Canu v2.2 (10), producing a circularized contig of 2,427,830 bp with 41.58% GC content. Gene predictions and annotations were performed using NCBI Prokaryotic Genome Annotation Pipeline v6.5 (11). The antibiotics and secondary metabolite analysis shell (antiSMASH) was used to mine biosynthetic gene clusters in the genome (12). Default parameters were used for all bioinformatics analyses. Table 1 provides the basic characteristics of this strain and genome.