Whole-genome sequences of 38 siderophore-producing isolates from root systems of two pea and one wheat varieties

TL;DR

This paper presents the whole-genome sequences of 38 bacteria that produce siderophores, isolated from the roots of pea and wheat plants.

Contribution

The study provides high-quality genomic data for 38 novel siderophore-producing bacterial isolates using PacBio HiFi sequencing.

Findings

PacBio HiFi sequencing generated 6.1 Gb of reads for the bacterial isolates.

The average assembly completeness across all isolates was 98.85%.

The isolates were obtained from the root systems of two pea and one wheat varieties.

Abstract

Here, we report the whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root systems of two pea and one wheat varieties. High-quality genomic data for each isolate was generated using PacBio HiFi sequencing, producing 6.1 Gb of HiFi reads and achieving an average assembly completeness of 98.85%.

Tables

TABLE 1. Taxonomic identification, related metadata, HiFi reads statistics, genome assembly statistics (BUSCO with the alphaproteobacteria_odb10 data set and QUAST), and accession numbers for the 38 bacterial whole-genome sequencesa

		Metadata		HiFi reads statistics		Genome assembly statistics							Accession numbers
Strain Codeb	Taxonomic Affiliation	Plant	Soil type	Read counts	N50 (bp)	BUSCOs Results	# Contigs	Total Length (bp)	N50 (bp)	L50	GC (%)	Coverage (×)	Biosample accession No.	SRA accession No.	Assembly accession No.
36a20	Acidovorax facilis	Wheat	Auzeville	21,525	14,783	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	3	5,809,211	5493086	1	64.34	40	SAMN47300670	SRX27953989	GCA_050627005.1
37c5	Acidovorax facilis	Wheat	Auzeville	42,293	11,357	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	3	5,806,590	5490465	1	64.34	61	SAMN47300673	SRX27954012	GCA_050626955.1
21a14	Arthrobacter sp. 21a14	Pea Dexter	Auzeville	25,977	10,022	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	2	5,652,313	5437079	1	61.55	35	SAMN47300684	SRX27953995	GCA_050627125.1
20a6	Arthrobacter sp. 20a6	Pea Dexter	Epoisses	16,628	10,117	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	3	5,655,880	5437081	1	61.55	22	SAMN47300702	SRX27954015	GCA_050710035.1
25a33	Enterobacter kobei	Pea Dexter	Auzeville	37,318	16,388	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4,762,226	4623341	1	55.01	94	SAMN47300682	SRX27953993	GCA_050627095.1
25b15	Enterobacter kobei	Pea Dexter	Auzeville	17,868	16,800	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4,762,226	4623341	1	55.01	46	SAMN47300685	SRX27953996	GCA_050627105.1
4a1	Enterobacter kobei	Pea Balltrap	Epoisses	15,809	15,755	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4,762,221	4623341	1	55.01	40	SAMN47300696	SRX27954008	GCA_050626945.1
9c6	Enterobacter kobei	Pea Balltrap	Auzeville	27,194	16,335	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4,762,226	4623341	1	55.01	71	SAMN47300678	SRX27954025	GCA_050626885.1
34a33	Enterobacter ludwigii	Wheat	Epoisses	12,914	15,383	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4983446	4881988	1	54.48	30	SAMN47300691	SRX27954003	GCA_050627035.1
4a6	Enterobacter ludwigii	Pea Balltrap	Epoisses	24,107	16,628	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4983447	4881989	1	54.48	61	SAMN47300697	SRX27954009	GCA_050626925.1
4b24	Enterobacter ludwigii	Pea Balltrap	Epoisses	26,176	16,314	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	4983447	4881989	1	54.48	65	SAMN47300698	SRX27954010	GCA_050626905.1
19b38	Enterobacter mori	Pea Dexter	Epoisses	26,063	7,611	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	8	4946610	4907588	1	55.49	31	SAMN47300703	SRX27954016	GCA_050710095.1
25c27	Enterobacter mori	Pea Dexter	Auzeville	26,278	16,097	C:100.0%[S:23.4%,D:76.6%],F:0.0%,M:0.0%,n:124	1	4911960	4911960	1	55.48	66	SAMN47300683	SRX27953994	GCA_050627085.1
25b30	Massilia eburnea	Pea Dexter	Auzeville	11,420	15,370	C:77.4%[S:77.4%,D:0.0%],F:2.4%,M:20.2%,n:124	36	4594051	163959	9	62.08	29	SAMN47300687	SRX27953998	GCA_050709955.1
10c5	Microbacterium phyllosphaerae	Pea Balltrap	Auzeville	90,071	14,152	C:98.4%[S:98.4%,D:0.0%],F:0.8%,M:0.8%,n:124	1	3826298	3826298	1	67.97	264	SAMN47300675	SRX27954022	GCA_050628115.1
8b26	Paenibacillus sp. 8b26	Pea Balltrap	Auzeville	28,221	18,206	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	1	6129587	6129587	1	46.44	62	SAMN47300680	SRX27953991	GCA_050626875.1
10c25	Paraburkholderia fungorum	Pea Balltrap	Auzeville	16,678	13,402	C:100.0%[S:97.6%,D:2.4%],F:0.0%,M:0.0%,n:124	6	9355406	4731166	1	61.74	17	SAMN47300676	SRX27954023	GCA_050710135.1
18a25	Paraburkholderia fungorum	Pea Dexter	Epoisses	24,018	14,819	C:100.0%[S:97.6%,D:2.4%],F:0.0%,M:0.0%,n:124	4	9322411	4729161	1	61.73	28	SAMN47300704	SRX27954017	GCA_050627395.1
25c37	Paraburkholderia fungorum	Pea Dexter	Auzeville	19,568	13,825	C:100.0%[S:97.6%,D:2.4%],F:0.0%,M:0.0%,n:124	4	9322396	4729159	1	61.73	21	SAMN47300686	SRX27953997	GCA_050627075.1
36b22	Polaromonas aquatica	Wheat	Auzeville	29,313	8,352	C:100.0%[S:99.2%,D:0.8%],F:0.0%,M:0.0%,n:124	1	4557853	4557853	1	61.59	41	SAMN47300672	SRX27954001	GCA_050626995.1
4a21	Pseudomonas alvandae	Pea Balltrap	Epoisses	15,580	14,932	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	1	6213704	6213704	1	60.96	27	SAMN47300699	SRX27954011	GCA_050626915.1
18b10	Pseudomonas brassicacearum	Pea Dexter	Epoisses	30,999	9,515	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	1	6739771	6739771	1	60.87	33	SAMN47300705	SRX27954018	GCA_050627145.1
22c22	Pseudomonas brassicacearum	Pea Dexter	Auzeville	24,495	9,452	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	2	6825820	6816008	1	60.81	25	SAMN47300688	SRX27953999	GCA_050710055.1
35a7	Pseudomonas gorinensis	Wheat	Epoisses	73,210	13,958	C:99.2%[S:99.2%,D:0.0%],F:0.8%,M:0.0%,n:124	2	7145029	7138193	1	60.51	114	SAMN47300692	SRX27954004	GCA_050709935.1
21c7	Pseudomonas gorinensis	Pea Dexter	Auzeville	96,544	13,640	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	1	7207491	7207491	1	60.48	142	SAMN47300689	SRX27954000	GCA_050627115.1
34a15	Pseudomonas gorinensis	Wheat	Epoisses	6,711	19,431	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	1	7206726	7206726	1	60.48	14	SAMN47300693	SRX27954005	GCA_050627045.1
9b17	Pseudomonas simiae	Pea Balltrap	Auzeville	36,437	8,757	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	2	6324885	6316763	1	60.28	39	SAMN47300677	SRX27954024	GCA_050709815.1
3c1	Pseudomonas siliginis	Pea Balltrap	Epoisses	113,858	13,435	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	1	5970447	5970447	1	60.04	195	SAMN47300700	SRX27954013	GCA_050626965.1
25b28	Pseudomonas solani	Pea Dexter	Auzeville	42,504	10,604	C:99.2%[S:99.2%,D:0.0%],F:0.8%,M:0.0%,n:124	3	7144013	3964255	1	65.89	48	SAMN47300690	SRX27954002	GCA_050709975.1
35c15	Pseudomonas thivervalensis	Wheat	Epoisses	11,620	16,943	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	1	6495419	6495419	1	61.22	22	SAMN47300694	SRX27954006	GCA_050627015.1
8a22	Pseudomonas thivervalensis	Pea Balltrap	Auzeville	9,214	12,166	C:99.2%[S:99.2%,D:0.0%],F:0.0%,M:0.8%,n:124	2	6979370	5539090	1	61.01	12	SAMN47300679	SRX27954026	GCA_050709855.1
4a18	Ralstonia holmesii	Pea Balltrap	Epoisses	5,942	14,080	C:98.4%[S:78.2%,D:3.2%],F:4.0%,M:14.6%,n:124	4	5578591	3593299	1	63.58	12	SAMN47300701	SRX27954014	GCA_050626935.1
18a19	Ralstonia insidiosa	Pea Dexter	Epoisses	9,068	14,820	C:100.0%[S:99.2%,D:0.8%],F:0.0%,M:0.0%,n:124	4	5999436	3744346	1	63.57	16	SAMN47300707	SRX27954020	GCA_050627405.1
18c12	Ralstonia insidiosa	Pea Dexter	Epoisses	9,113	14,582	C:100.0%[S:99.2%,D:0.8%],F:0.0%,M:0.0%,n:124	4	6739771	6739771	1	60.87	16	SAMN47300706	SRX27954019	GCA_050627135.1
37a14	Ralstonia thomasii	Wheat	Auzeville	10,129	15,860	C:99.2%[S:98.4%,D:0.8%],F:0.8%,M:0.0%,n:124	3	5138688	3497269	1	63.80	23	SAMN47300674	SRX27954021	GCA_050626975.1
37a16	Roseateles noduli	Wheat	Auzeville	11,881	14,537	C:98.2%[S:24.2%,D:0.0%],F:5.6%,M:70.2%,n:124	1	6630955	6630955	1	68.53	20	SAMN47300671	SRX27953990	GCA_050626985.1
35b25	Variovorax paradoxus NBRC 15149	Wheat	Epoisses	53,373	11,279	C:100.0%[S:100.0%,D:0.0%],F:0.0%,M:0.0%,n:124	2	6043317	5556705	1	64.82	76	SAMN47300695	SRX27954007	GCA_050627025.1
8a8	Variovorax paradoxus NBRC 15149	Pea Balltrap	Auzeville	7,620	16,223	C:98.4%[S:98.4%,D:0.0%],F:0.8%,M:0.8%,n:124	2	6299093	5159596	1	66.30	15	SAMN47300681	SRX27953992	GCA_050626895.1

Full text

ANNOUNCEMENT

Iron is abundant in soils but mostly unavailable to plants and microorganisms (1). Many bacteria secrete siderophores—iron-chelating secondary metabolites—that facilitate iron acquisition and enhance plant uptake (2–4). Beyond nutrition, siderophores mediate microbial communities' interactions, including cooperation, competition, and exploitation, influencing community assembly, stability, and plant health (5, 6).

Here, we report whole-genome sequencing of 38 siderophore-producing bacterial strains isolated from the root system of two pea (Pisum sativum L., Balltrap and Dexter) and one wheat (Triticum aestivum L., Flamenko) varieties (7). Plants were grown in two previously characterized soil types (7) under laboratory conditions (47°19′1.268″ N, 5°4′16.075″ E). Roots were rinsed, crushed, and serial dilutions plated on 0.1× Tryptic Soy Agar (TSA, Condalab) supplemented with 200 µg mL^−1^ cycloheximide (Sigma). Plates were incubated at 25°C for 5 days. Colonies were purified by single-colony isolation and screened for siderophore production using CAS medium (8, 9). Positive isolates were coded (Table 1) and stored at −80°C in 0.1× Tryptic Soy Broth (TSB, Condalab) with 12.5% glycerol (Promega), after 3–5 days of liquid growth.

For DNA extraction, strains were recultivated in 0.1 × TSB and harvested at the end of exponential phase. Genomic DNA was extracted using Genomic-tip 20 /G Kit (Qiagen), quantified with Qubit dsDNA HS (ThermoFisher), and quality-checked by Nanodrop (ThermoFisher) and Agilent Fragment Analyzer (DNA 50 kb kit) (TECAN Infinite 200 Pro). Two µg of DNA per sample were purified and sheared to ~10 kb, using either FastPrep96 (MP Biomedicals) or Megaruptor 3 (Diagenode); no size selection followed shearing.

Libraries were prepared from 500  ng sheared DNA using the SMRTbell Express Template Prep Kit 2.0 (PacBio), ligated with barcoded blunt-end hairpin adapters, treated with exonucleases, and pooled equimolarly.

Sequencing was performed on the PacBio Sequel II system using the Binding Kit 3.2 and Sequencing Kit 2.0, with 100 pM loading concentration, two-hours pre-extension, and 30 hours movie per SMRT cell (3 cells total), using Sequel II DNA Polymerase 2.2.

Subreads were processed using SMRT Link to generate Circular Consensus Sequences (CCS, or HiFi reads), with automatic adapter removal and Q ≥ 20 filtering, generating 6.1 Gb of HiFi reads. Read counts and N50 values are in Table 1.

HiFi reads were assembled with Flye v. 2.9.5 (10). Assembly quality was assessed with BUSCO v5.7.1 (11) with alphaproteobacteria_odb10 data set (11) and QUAST v5.2.0 (12), showing an average completeness of 98.85% (range: 77.40% - 100.00%) and average genome size of 6,067,693 bp (range: 3,826,298 bp - 9,355,406 bp). Chromosomes and plasmids were identified using BLAST v2.16.0. Single-contig assemblies were confirmed circular by Flye reports and submitted as complete genomes to NCBI. Taxonomic classification used Kraken2 v2.1.2 (13) and GTDB-Tk v2.4.0 (14). Assembly summaries are in Table 1.

Genome mining with antiSMASH v7.0 (15) identified 203 biosynthetic gene clusters across the 38 strains, linked to 51 putative secondary metabolites. Sixteen distinct siderophore compounds were annotated via the SIDERITE database (16), including alcaligin, enterobactin, aerobactin, pyoverdine, pyochelin, cepaciachelin, staphyloferrin B, malleobactin, variochelin, desferrioxamine, corrugatin, turnerbactin, methanobactin, histicorrugatin, delftibactin, and pacifibactin.