Complete genome sequence of Gluconobacter frateurii ML.ISBL3, an endophytic strain isolated from aerial roots of Syngonium podophyllum

TL;DR

This paper reports the complete genome sequence of Gluconobacter frateurii ML.ISBL3, an endophytic bacterium found in the aerial roots of Syngonium podophyllum.

Contribution

The novel contribution is the complete genome sequence of an endophytic Gluconobacter frateurii strain isolated from Syngonium podophyllum.

Findings

The genome consists of a single chromosome of 3,309,710 bp.

The genome was assembled using a hybrid assembly approach.

The G+C content of the genome is 56.30%.

Abstract

The endophytic strain Gluconobacter frateurii ML.ISBL3 was isolated from aerial roots of Syngonium podophyllum in Hong Kong. Its complete genome, established through hybrid assembly, comprises a single chromosome of 3,309,710 bp (56.30% G+C).

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ANNOUNCEMENT

The partial aerobic oxidations of sugars and alcohols to acetic acid by family Acetobacteraceae (1) find use in industrial biotransformations and biosensors (2, 3), although some strains produce valuable exopolysaccharides (4). Gluconobacter spp., however, accumulate gluconic acid rather than acetate (5) via membrane-bound pyrroloquinoline-quinone-dependent dehydrogenases (6). Preferring sugar-rich and relatively low-nitrogen environments (1), Gluconobacter spp. are commonly associated with plants (7–9), plant-feeding insect guts (10), and the spoilage of soft drinks and juices (11, 12); only rarely are they sources of infection (13, 14).

Here, G. frateurii ML.ISBL3 was isolated from aerial roots of Syngonium podophyllum in Hong Kong (22.266462N 114.130191E; on 25 June 2021) as a potential symbiont to this successful oligotroph: 20 mm lengths of root tips were surface sterilized using 1% (wt:vol) 8-hydroxyquinoline sulphate before incubation in nitrogen-free Jensen’s broth M710 (15, 16) for 7 days at 32°C. Following subculture to fresh M710 broth and incubation under the same conditions, 100 µL aliquots were spread on M710 agar and Pikovskaya’s agar (17). ML.ISBL3 produces large, clear, mucoid colonies on both media, as well as clear zones on Pikovskaya’s agar. The isolate does not grow well on Luria agar (18), so a single colony taken from M710 agar was passaged to purity on the same medium before streaking onto V8 agar (https://wiki.bugwood.org/V8_agar) for overnight growth before harvesting for DNA extraction (DNeasy PowerSoil Pro Kit, Qiagen GmbH, Hilden, Germany, following manufacturer’s protocol). All agar incubations conducted at 27°C.

Paired-end short-read sequencing libraries were prepared using a NexteraXT DNA Library Preparation Kit (Illumina, Inc., USA) and sequenced via the Illumina MiSeq platform using v3 chemistry (2 × 300 bp). A total of 673,771 raw read pairs were quality filtered and trimmed using TrimGalore! v0.6.7 (https://github.com/FelixKrueger/TrimGalore) (stringency:3; -e:0.2), producing 669,098 read pairs (median length 172 bp) totaling ~237.2 Mbp (SRX21353896). Long-read libraries, prepared from the same extracted DNA using the Rapid Barcoding Kit SQK-RBK004 (without size selection), were sequenced via Oxford Nanopore’s Spot-ON Flow Cell (vR9), MinION sequencer, and MinKNOW v3.1.8 software, with base-calling by Guppy v2.1.3 high-accuracy mode. The final long-read data set of 326,952 reads (N50 10,361) was trimmed by Filtlong v0.2.1 (https://github.com/rrwick/Filtlong) (min_length: 2,000; target_bases: 500 Mbp; length_weight: 10) selecting 81,999 reads (500 Mbp; median length 4,609 bp, N50 7,586) (SRX21353897) to scaffold the assembly. Default parameters were used for all software unless otherwise specified.

Hybrid assembly, overlap removal, and sequence rotation were performed by Unicycler v0.4.8-beta (19) to yield a single circular chromosome of 3,309,710 bp (56.30% G + C; 151× coverage, rotated to begin M9M3E7_GLUTH dnaA) judged 100% complete (0% contamination) by CheckM v1.1.6 (20) that was submitted to NCBI PGAP v6.0 (21) for annotation. JSpecies v4.1.1 (22) found ML.ISBL3 closest to Gluconobacter frateurii strain NBRC 3264 (BEWN01000000.1) with an average nucleotide identity of 96.91% [ANIb by BLAST +2.2.29 (23)].

PGAP predicts a type 1-levansucrase (24) encoded at locus MKW11_04725, with levanase at MKW11_05395. Similarly, the chemotaxis gene cluster (che1) (MKW11_07970–08005) and hopanoid biosynthesis operon hpnABCDEFG (MKW11_14220–14260) may support root invasion (25–27), and 1-aminocyclopropane-1-carboxylate deaminase (MKW11_07600) and the pqqABCDE operon (MKW11_05315–05295) may promote plant growth (28–30).