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Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection
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Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection
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Abstract and figures
Achromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa. Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been documented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the complete genome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucumber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq and contained 6,930,067 nucleotides with 67.55% G + C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, including those associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity. Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plant growth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpea is discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizosphere in sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security.
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Vol.:(0123456789)Current Microbiology (2024) 81:356https://doi.org/10.1007/s00284-024-03882-8SHORT COMMUNICATIONComplete Genome of Achromobacter xylosoxidans, a Nitrogen‑FixingBacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp)Tolerant to Cucumber Mosaic Virus InfectionAdedapo O. Adediji1  · James A. Ojo2  · Adebayo A. Olowoake2  · Khadijat O. Alabi2  · Gabriel I. Atiri3Received: 5 February 2024 / Accepted: 3 September 2024© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024AbstractAchromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa.Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been docu-mented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the completegenome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucum-ber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq andcontained 6,930,067 nucleotides with 67.55% G+ C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, includingthose associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity.Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plantgrowth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpeais discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizospherein sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security.IntroductionCowpea is an economically important legume crop grownwidely and cultivated across sub-Saharan Africa because ofits nutritional value and ability to improve marginal soilsthrough its association with diazotrophic bacteria. One of thenumerous bacterial species associated with cowpea rhizo-sphere is Achromobacter xylosoxidans, a gram-negative,aerobic bacteria belonging to the family Alcaligenaceae. Ithas been reported to increase the productivity of cowpea [1]and other crops [2] while stimulating systemic resistanceagainst plant pathogens [3]. Cucumber mosaic virus (CMV),a cosmopolitan plant virus associated with huge yield lossesin several plant hosts worldwide [4–6], affects cowpea pro-duction especially when susceptible varieties are grown [7].Integrated management of CMV infections with the use ofvirus-resistant varieties and stimulation of systemic resist-ance remains a vital strategy for optimal crop yield. Soil-colonizing bacteria such as A. xylosoxidans can increase soilfertility and promote plant growth despite biotic and abioticstress [8]. Its growth-promoting activity has been linked toits high nitrogenase and phosphate solubilization ability aswell as the production of Indole3-acetic acid (IAA) [9].Despite the importance and potential of A. xylosoxidansto increase soil fertility in marginal soils across Africa, verylittle information is available on its complete genetic proper-ties as a veritable plant growth-promoting bacteria. There-fore, there is a need to obtain more genomic information onA. xylosoxidans to understand its role and usefulness withinthe cowpea rhizosphere. Here, we characterized the genomesequence of A. xylosoxidans strain DDA01 associated with aCMV-tolerant cowpea variety grown in Nigeria, the world’slargest producer of cowpea. This genomic information pro-vides better insights into soil fertility options to ensure foodsecurity in sub-Saharan Africa.* Adedapo O. Adedijiadedapo.adediji@paulesi.org.ng1 Research Office, Pan African University Life and EarthSciences Institute (Including Health and Agriculture),Ibadan, Nigeria2 Department of Crop Production, Kwara State University,Malete, Ilorin, Nigeria3 Department of Crop Protection and Environmental Biology,University of Ibadan, Ibadan, Nigeria
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A. O. Adediji et al.356 Page 2 of 7Materials and MethodsIn December 2022, cowpea plants established in Ibadan,Nigeria (7.40 N, 3.85 E) showed varied tolerance toCMV infection due to the activity of plant growth-pro-moting bacteria (data not shown). Thus, topsoil was col-lected from the rhizosphere of CMV-tolerant cowpeavariety ‘SAMPEA-7’ to characterize DDA01, the plantgrowth-promoting bacteria present in the soil. DDA01was isolated via the method described by Reinecke et al.[10]. Cultivation was performed in 0.8% (w/v) nutrientbroth medium and incubated aerobically at 30 °C on arotary shaker (130–150  rpm). The bacterial DNA wasextracted using the ZymoBIOMICS DNA Miniprep Kit(Zymo, Irvine, CA, USA) according to the manufactur-er’s instructions. Initial identification of A. xylosoxidansstrain DDA01 was carried out via PCR with primers tar-geting the universal bacterial 16S rRNA region [11] andthe nrdA gene, which is specific to A. xylosoxidans [12].All reactions were performed in total volumes of 50 μlcontaining 2 × GoTaq® Flexi Buffer (Promega, Madison,WI, USA) 0.2 mM dNTPs (NEB, Ipswich, MA, USA),1.5 mM MgCl2 (Promega, Madison, WI, USA), 10 μM ofeach primer (Inqaba, Pretoria, South Africa), and 50 ngof extracted DNA. The amplification conditions were setat 94 °C for 4 min, 35 cycles of 94 °C for 30 s, 52 °C(both primer pairs) for 45 s, and 72 °C for 45 s, and a finalelongation at 72 °C for 10 min. The amplified productswere ethanol purified and bidirectionally cycle sequencedwith ABI BigDye Terminator v3.1 (Applied Biosystems,USA). Both the 16S rRNA and nrdA gene sequences werebase called in BioEdit v.7.2.3 [13], analysed via nBLASTin GenBank database and confirmed as A. xylosoxidans.The genomic DNA from DDA01 was further processed.First, Illumina-specific adapter sequences were ligated toeach amplicon using the NEBNext Ultra II DNA libraryprep kit. The sequencing run was then performed on anIllumina MiSeq platform, generating 300 bp paired-endreads using a MiSeq v3 (600 cycle) kit. The whole genomeassembly was conducted using the assembler ABySS v.2 [14] with multiple-Kmer parameters. Assembly qual-ity was assessed via Quast v5.2.0 [15]. The annotationof DDA01 was performed via the automated ProkaryoticGenome Annotation Platform (PGAP) within the NCBIframework (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The circular genome of DDA01 was con-structed using DNA Plotter on Artemis 18.2.0 [16]. TheGC content profile was determined using GC-Profilev2.0 [17]. Gene clusters that encode secondary metabo-lites were examined via antiSMASH v6.0 with defaultparameters [18]. Investigations into antibiogram andantimicrobial resistance genes were conducted using the5NosoAE server [19]. Genomic islands were identifiedwith IslandViewer v4 [20] using three methods: SIGI-HMM, Islandpick and IslandPath-DIMOB, with defaultparameters. Putative clustered regularly interspaced shortpalindromic repeats (CRISPR) elements were predictedby CRISPRCasFinder with default parameters (https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index). Thetandem repeats were scanned via RepeatMasker (http://Fig. 1 Circular genome map ofA. xylosoxidans strain DDA01with the first and second outer-most rings depicting protein-coding genes on the forwardand reverse strands, respec-tively. The third, fourth andfifth rings show the locationsof the misc features, tRNA andrRNA genes on the forward andreverse strands, respectively.The grey and brown plots depictthe GC content, with the peaksextending outwards from thecircle circumference represent-ing a GC content above thegenome average, whereas thoseextending inwards from thecircle circumference representssegments with a GC contentlower than the genome average.The innermost gold and purpleplots depict the GC skew. Basecomposition plots were gener-ated via a sliding window of69,000 nucleotides (Color figureonline)
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